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/7916153/working'
mkdir: created directory `/scratch/stefan/7916153/working/protonate'
Storing results in /scratch/stefan/7916153/finished
Working in /scratch/stefan/7916153/working
/scratch/stefan/7916153/working /scratch/stefan/7916153

/scratch/stefan/7916153/working/protonate /scratch/stefan/7916153/working /scratch/stefan/7916153
Precomputing protomers for all compounds (pH: 7.4)
awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory)
rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory
awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory)
awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory)
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: 1063 protomers created
Coalesing and merging protomers
1023 protomers generated for 1000 compounds
Checking for new stereocenters and expanding
1029 protomers after new stereo-center expansion
/scratch/stefan/7916153/working /scratch/stefan/7916153

Bulk generating 3D conformations all protomers in /scratch/stefan/7916153/working/3D
mkdir: created directory `/scratch/stefan/7916153/working/3D'
We are using corina for 3D embeding
debuging info:: /scratch/stefan/7916153/working/protonate/xaaaabh-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'
1030 3D conformations generated for 1000 compounds

Building REAL250005070893
mkdir: created directory `/scratch/stefan/7916153/working/building'
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070893'
/scratch/stefan/7916153/working/building/REAL250005070893 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070893

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070893/0 /scratch/stefan/7916153/working/building/REAL250005070893 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1
`/scratch/stefan/7916153/working/3D/1' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](O)C2)

`REAL250005070893.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070893.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070893/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070893 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](O)C2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.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, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [32, 7, 32, 32, 117, 190, 190, 190, 201, 201, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 117, 117, 190, 201, 7, 1, 1, 3, 1, 1] 603
rigid atoms, others: [32, 33, 35, 36, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 34])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070893 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](O)C2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.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, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [82, 32, 83, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 83, 111, 111, 111, 201, 201, 201, 201, 201, 201, 201, 83, 83, 83, 32, 32, 10, 1, 111, 201, 201, 603, 201, 201] 603
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36])
total number of confs: 1152
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070893 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070893
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `/scratch/stefan/7916153/finished'
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070893/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070893
Building REAL250005070894
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070894'
/scratch/stefan/7916153/working/building/REAL250005070894 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070894

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070894/0 /scratch/stefan/7916153/working/building/REAL250005070894 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 2)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/2
`/scratch/stefan/7916153/working/3D/2' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C12CC(C1)CO2)

`REAL250005070894.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070894.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070894/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070894 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C12CC(C1)CO2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [34, 10, 34, 34, 91, 131, 131, 131, 142, 142, 142, 142, 142, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 34, 34, 91, 91, 131, 142, 10, 1, 1, 1, 1, 1, 1, 1] 142
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 510
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070894 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C12CC(C1)CO2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [78, 36, 80, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 80, 114, 114, 114, 142, 142, 142, 142, 142, 80, 80, 80, 36, 36, 10, 1, 114, 142, 142, 142, 142, 142, 142, 142] 142
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])
total number of confs: 477
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070894 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070894
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070894/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070894
Building REAL250005070895
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070895'
/scratch/stefan/7916153/working/building/REAL250005070895 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070895

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070895/0 /scratch/stefan/7916153/working/building/REAL250005070895 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 3)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/3
`/scratch/stefan/7916153/working/3D/3' -> `0.mol2'
Preparing input files

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

`REAL250005070895.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070895.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070895/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070895 none CCC=CC=CC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 148, 148, 135, 135, 65, 65, 65, 46, 16, 46, 46, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 148, 148, 135, 135, 65, 46, 46, 46, 16, 16, 4, 1] 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])
total number of confs: 824
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070895 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070895
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070895/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070895
Building REAL250005070896
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070896'
/scratch/stefan/7916153/working/building/REAL250005070896 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070896

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070896/0 /scratch/stefan/7916153/working/building/REAL250005070896 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 4)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/4
`/scratch/stefan/7916153/working/3D/4' -> `0.mol2'
Preparing input files

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

`REAL250005070896.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070896.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070896/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070896 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN(C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 5, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [35, 13, 35, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 58, 58, 58, 82, 93, 93, 100, 100, 35, 35, 35, 13, 13, 4, 1, 58, 82, 82, 93, 93, 93, 100, 100] 100
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])
total number of confs: 406
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070896 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070896
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070896/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070896
Building REAL250005070897
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070897'
/scratch/stefan/7916153/working/building/REAL250005070897 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070897

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070897/0 /scratch/stefan/7916153/working/building/REAL250005070897 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 5)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/5
`/scratch/stefan/7916153/working/3D/5' -> `0.mol2'
Preparing input files

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

`REAL250005070897.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070897.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070897/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070897 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC(=O)N[N-]1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'N.2', '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, 8, 1, 11, 1, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 6, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [32, 13, 32, 32, 57, 72, 72, 72, 82, 82, 82, 82, 82, 13, 1, 13, 1, 1, 1, 1, 1, 1, 32, 32, 32, 57, 57, 72, 82, 13, 1] 82
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 316
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070897 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC(=O)N[N-]1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'N.2', '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, 8, 1, 11, 1, 8, 1, 11, 8, 8, 7, 7, 7, 7, 7, 6, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [45, 29, 45, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 45, 53, 53, 53, 82, 82, 82, 82, 82, 45, 45, 45, 29, 29, 9, 1, 53, 82] 82
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])
total number of confs: 262
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070897 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070897
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070897/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070897
Building REAL250005070898
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070898'
/scratch/stefan/7916153/working/building/REAL250005070898 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070898

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070898/0 /scratch/stefan/7916153/working/building/REAL250005070898 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 6)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/6
`/scratch/stefan/7916153/working/3D/6' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(F)CC1)

`REAL250005070898.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070898.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070898/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070898 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(F)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', '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, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [42, 10, 42, 42, 114, 160, 160, 160, 165, 165, 165, 165, 165, 10, 1, 10, 1, 1, 1, 1, 42, 42, 42, 114, 114, 160, 165, 10, 1, 1, 1, 1] 165
rigid atoms, others: [14, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 599
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070898 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(F)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', '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, 8, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [75, 28, 76, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 76, 105, 105, 105, 165, 165, 165, 76, 76, 76, 28, 28, 9, 1, 105, 165, 165, 165, 165] 165
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 590
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070898 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070898
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070898/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070898
Building REAL250005070899
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070899'
/scratch/stefan/7916153/working/building/REAL250005070899 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070899

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070899/0 /scratch/stefan/7916153/working/building/REAL250005070899 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 7)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/7
`/scratch/stefan/7916153/working/3D/7' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(O)C1CC1)

`REAL250005070899.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070899.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070899/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070899 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [85, 36, 85, 85, 154, 198, 198, 198, 201, 201, 201, 201, 201, 36, 9, 36, 1, 9, 9, 1, 1, 1, 85, 85, 85, 154, 154, 198, 201, 36, 9, 9, 9, 27, 1, 1, 1, 1, 1] 603
rigid atoms, others: [34, 35, 36, 37, 38, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 812
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070899 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [67, 24, 69, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 69, 112, 112, 112, 189, 189, 189, 201, 201, 69, 69, 69, 24, 24, 8, 1, 112, 189, 189, 189, 567, 201, 201, 201, 201, 201] 603
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: 1400
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070899 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070899
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070899/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070899
Building REAL250005070900
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070900'
/scratch/stefan/7916153/working/building/REAL250005070900 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070900

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070900/0 /scratch/stefan/7916153/working/building/REAL250005070900 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 8)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/8
`/scratch/stefan/7916153/working/3D/8' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=C(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)O1)

`REAL250005070900.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070900.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070900/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070900 none CC1=NC=C(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 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, 85, 85, 85, 54, 24, 54, 54, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 85, 54, 54, 54, 24, 24, 8, 1] 91
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])
total number of confs: 325
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070900 none CC1=NC=C(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 51, 89, 89, 89, 91, 91, 91, 91, 91, 1, 2, 2, 2, 1, 6, 19, 19, 19, 51, 51, 89, 91] 91
rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 330
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070900 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070900
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070900/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070900
Building REAL250005070901
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070901'
/scratch/stefan/7916153/working/building/REAL250005070901 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070901

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070901/0 /scratch/stefan/7916153/working/building/REAL250005070901 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 9)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/9
`/scratch/stefan/7916153/working/3D/9' -> `0.mol2'
Preparing input files

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

`REAL250005070901.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070901.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070901/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070901 none COC(C)(C)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', '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', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 123, 200, 200, 123, 123, 76, 28, 76, 74, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 200, 200, 200, 200, 200, 123, 76, 76, 76, 28, 28, 7, 1] 201
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: 832
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070901 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070901
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070901/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070901
Building REAL250005070902
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070902'
/scratch/stefan/7916153/working/building/REAL250005070902 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070902

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070902/0 /scratch/stefan/7916153/working/building/REAL250005070902 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 10)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/10
`/scratch/stefan/7916153/working/3D/10' -> `0.mol2'
Preparing input files

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

`REAL250005070902.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070902.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070902/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070902 none CC(CC#N)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', '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', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [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]
0  hydrogens 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, 87, 168, 201, 201, 87, 87, 50, 16, 50, 50, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 201, 201, 87, 50, 50, 50, 16, 16, 6, 1] 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])
total number of confs: 864
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070902 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070902
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070902/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070902
Building REAL250005070903
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070903'
/scratch/stefan/7916153/working/building/REAL250005070903 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070903

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070903/0 /scratch/stefan/7916153/working/building/REAL250005070903 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 11)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/11
`/scratch/stefan/7916153/working/3D/11' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1CC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005070903.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070903.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070903/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070903 none CCC1CC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [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
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [191, 191, 191, 191, 138, 138, 138, 84, 32, 84, 82, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 191, 191, 191, 191, 191, 191, 191, 191, 191, 138, 84, 84, 84, 32, 32, 9, 1] 191
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: 700
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070903 none CCC1CC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [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
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 9, 9, 9, 36, 36, 36, 109, 179, 179, 179, 191, 191, 191, 191, 191, 2, 2, 2, 2, 2, 1, 1, 1, 1, 9, 36, 36, 36, 109, 109, 179, 191] 191
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])
total number of confs: 686
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070903 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070903
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070903/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070903
Building REAL250005070904
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070904'
/scratch/stefan/7916153/working/building/REAL250005070904 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070904

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070904/0 /scratch/stefan/7916153/working/building/REAL250005070904 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 12)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/12
`/scratch/stefan/7916153/working/3D/12' -> `0.mol2'
Preparing input files

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

`REAL250005070904.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070904.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070904/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070904 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](C)C(C)(C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
225  conformations in input
total number of sets (complete confs): 225
using faster count positions algorithm for large data
unique positions, atoms: [35, 13, 35, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 35, 49, 49, 49, 65, 65, 65, 75, 72, 75, 35, 35, 35, 13, 13, 6, 1, 49, 65, 65, 65, 75, 75, 75, 75, 75, 75, 225] 225
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 559
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070904 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070904
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070904/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070904
Building REAL250005070905
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070905'
/scratch/stefan/7916153/working/building/REAL250005070905 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070905

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070905/0 /scratch/stefan/7916153/working/building/REAL250005070905 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 13)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/13
`/scratch/stefan/7916153/working/3D/13' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(=O)O1)

`REAL250005070905.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070905.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070905/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070905 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(=O)O1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'O.3', '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, 8, 1, 11, 5, 5, 12, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 5, 3, 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: [36, 10, 36, 36, 99, 144, 144, 144, 155, 155, 155, 155, 155, 10, 1, 10, 1, 1, 1, 1, 1, 1, 36, 36, 36, 99, 99, 144, 155, 10, 1, 1, 1] 155
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 556
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070905 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(=O)O1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'O.3', '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, 8, 1, 11, 5, 5, 12, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 5, 3, 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: [73, 27, 75, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 75, 109, 109, 109, 155, 155, 155, 155, 155, 75, 75, 75, 27, 27, 10, 1, 109, 155, 155, 155] 155
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])
total number of confs: 569
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070905 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070905
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070905/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070905
Building REAL250005070906
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070906'
/scratch/stefan/7916153/working/building/REAL250005070906 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070906

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070906/0 /scratch/stefan/7916153/working/building/REAL250005070906 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 14)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/14
`/scratch/stefan/7916153/working/3D/14' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C12CC(C1)OC2)

`REAL250005070906.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070906.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070906/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070906 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C12CC(C1)OC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 7, 36, 36, 117, 191, 191, 191, 201, 201, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 36, 36, 36, 117, 117, 191, 201, 7, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 694
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070906 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C12CC(C1)OC2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 22, 59, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 59, 67, 67, 67, 201, 201, 201, 201, 201, 59, 59, 59, 22, 22, 8, 1, 67, 201, 201, 201, 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])
total number of confs: 438
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070906 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070906
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070906/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070906
Building REAL250005070907
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070907'
/scratch/stefan/7916153/working/building/REAL250005070907 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070907

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070907/0 /scratch/stefan/7916153/working/building/REAL250005070907 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 15)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/15
`/scratch/stefan/7916153/working/3D/15' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C1CC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005070907.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070907.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070907/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070907 none CC(O)C1CC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 4, 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]
1  hydrogens 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, 171, 201, 171, 171, 71, 71, 71, 47, 17, 47, 47, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 171, 171, 171, 171, 71, 47, 47, 47, 17, 17, 6, 1] 603
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: 1320
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070907 none CC(O)C1CC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 4, 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]
1  hydrogens 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, 1, 1, 1, 1, 13, 13, 13, 38, 38, 38, 98, 166, 166, 166, 171, 171, 171, 171, 171, 5, 5, 5, 5, 15, 1, 1, 1, 1, 13, 38, 38, 38, 98, 98, 166, 171] 603
rigid atoms, others: [1, 3, 4, 5, 6, 27, 28, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 647
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070907 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070907
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070907/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070907
Building REAL250005070908
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070908'
/scratch/stefan/7916153/working/building/REAL250005070908 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070908

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070908/0 /scratch/stefan/7916153/working/building/REAL250005070908 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 16)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/16
`/scratch/stefan/7916153/working/3D/16' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](C)C2)

`REAL250005070908.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070908.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070908/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070908 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](C)C2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 7, 34, 34, 115, 191, 191, 191, 201, 201, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 115, 115, 191, 201, 7, 1, 1, 2, 2, 2, 1, 1] 201
rigid atoms, others: [32, 33, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36])
total number of confs: 720
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070908 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](C)C2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 72, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 72, 104, 104, 104, 201, 201, 201, 201, 201, 201, 201, 72, 72, 72, 26, 26, 7, 1, 104, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 526
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070908 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070908
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070908/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070908
Building REAL250005070909
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070909'
/scratch/stefan/7916153/working/building/REAL250005070909 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070909

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070909/0 /scratch/stefan/7916153/working/building/REAL250005070909 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 17)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/17
`/scratch/stefan/7916153/working/3D/17' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NC=N1)

`REAL250005070909.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070909.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070909/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070909 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NC=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [88, 47, 88, 88, 162, 197, 197, 197, 201, 201, 201, 201, 201, 47, 9, 47, 1, 1, 1, 1, 1, 1, 88, 88, 88, 162, 162, 197, 201, 47, 9, 9, 1, 1] 201
rigid atoms, others: [32, 33, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 796
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070909 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NC=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [59, 24, 59, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 59, 88, 88, 88, 166, 201, 201, 201, 201, 59, 59, 59, 24, 24, 8, 1, 88, 166, 166, 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])
total number of confs: 726
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070909 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070909
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070909/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070909
Building REAL250005070910
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070910'
/scratch/stefan/7916153/working/building/REAL250005070910 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070910

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070910/0 /scratch/stefan/7916153/working/building/REAL250005070910 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 18)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/18
`/scratch/stefan/7916153/working/3D/18' -> `0.mol2'
Preparing input files

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

`REAL250005070910.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070910.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070910/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070910 none CC(C[NH+](C)C)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 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
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 12, 12, 12, 12, 11, 11, 9, 7, 9, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 11, 9, 9, 9, 7, 7, 4, 1] 12
rigid atoms, others: [42, 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, 40, 41])
total number of confs: 47
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070910 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070910
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070910/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070910
Building REAL250005070911
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070911'
/scratch/stefan/7916153/working/building/REAL250005070911 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070911

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070911/0 /scratch/stefan/7916153/working/building/REAL250005070911 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 19)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/19
`/scratch/stefan/7916153/working/3D/19' -> `0.mol2'
Preparing input files

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

`REAL250005070911.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070911.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070911/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070911 none C=CC(C)(O)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.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', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 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]
1  hydrogens 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, 201, 157, 157, 92, 31, 92, 88, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 157, 92, 92, 92, 31, 31, 7, 1] 603
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])
total number of confs: 1430
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070911 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070911
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070911/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070911
Building REAL250005070912
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070912'
/scratch/stefan/7916153/working/building/REAL250005070912 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070912

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070912/0 /scratch/stefan/7916153/working/building/REAL250005070912 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 20)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/20
`/scratch/stefan/7916153/working/3D/20' -> `0.mol2'
Preparing input files

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

`REAL250005070912.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070912.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070912/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070912 none CCC(C)(CO)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 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: [174, 145, 93, 145, 145, 197, 93, 93, 55, 23, 55, 55, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 183, 183, 183, 183, 183, 145, 145, 145, 197, 197, 591, 93, 55, 55, 55, 23, 23, 9, 1] 603
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: 1718
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070912 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070912
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070912/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070912
Building REAL250005070913
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070913'
/scratch/stefan/7916153/working/building/REAL250005070913 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005070913

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070913/0 /scratch/stefan/7916153/working/building/REAL250005070913 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 21)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/21
`/scratch/stefan/7916153/working/3D/21' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1([NH+](C)C)CC1)

`REAL250005070913.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070913.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070913/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070913 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1([NH+](C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [4, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 3, 3, 3, 1, 1, 4, 4, 4, 4, 4, 4, 5, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1] 5
rigid atoms, others: [37, 38, 39, 40, 14, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 24
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070913 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1([NH+](C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 5
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 15
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070913 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005070913/1 /scratch/stefan/7916153/working/building/REAL250005070913 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 22)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/22
`/scratch/stefan/7916153/working/3D/22' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(N(C)C)CC1)

`REAL250005070913.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005070913.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070913/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070913 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(N(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [15, 6, 15, 15, 37, 58, 58, 58, 62, 62, 62, 62, 62, 6, 1, 6, 1, 1, 4, 4, 1, 1, 15, 15, 15, 37, 37, 58, 62, 6, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 62
rigid atoms, others: [36, 37, 38, 39, 14, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 221
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070913 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(N(C)C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [35, 18, 35, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 35, 45, 45, 45, 62, 62, 62, 62, 62, 35, 35, 35, 18, 18, 7, 1, 45, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62] 62
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, 39])
total number of confs: 236
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070913 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070913
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005070913/1.*
0: /scratch/stefan/7916153/working/building/REAL250005070913/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070913
Building REAL250005070914
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070914'
/scratch/stefan/7916153/working/building/REAL250005070914 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070914

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070914/0 /scratch/stefan/7916153/working/building/REAL250005070914 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 23)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/23
`/scratch/stefan/7916153/working/3D/23' -> `0.mol2'
Preparing input files

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

`REAL250005070914.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070914.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070914/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070914 none CCCC=CC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', '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', 'H', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [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, 166, 114, 114, 46, 46, 46, 30, 13, 30, 30, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 166, 166, 114, 114, 46, 30, 30, 30, 13, 13, 4, 1] 201
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: 869
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070914 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070914
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070914/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070914
Building REAL250005070915
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070915'
/scratch/stefan/7916153/working/building/REAL250005070915 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070915

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070915/0 /scratch/stefan/7916153/working/building/REAL250005070915 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 24)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/24
`/scratch/stefan/7916153/working/3D/24' -> `0.mol2'
Preparing input files

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

`REAL250005070915.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070915.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070915/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070915 none CC=C(F)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 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', '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, 1, 1, 15, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [101, 101, 87, 101, 87, 87, 67, 28, 67, 66, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 87, 67, 67, 67, 28, 28, 10, 1] 101
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])
total number of confs: 387
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070915 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070915
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070915/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070915
Building REAL250005070916
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070916'
/scratch/stefan/7916153/working/building/REAL250005070916 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070916

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070916/0 /scratch/stefan/7916153/working/building/REAL250005070916 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 25)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/25
`/scratch/stefan/7916153/working/3D/25' -> `0.mol2'
Preparing input files

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

`REAL250005070916.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070916.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070916/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070916 none CCC(C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)C(C)C 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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [172, 170, 99, 99, 99, 69, 29, 69, 69, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 170, 196, 192, 182, 182, 182, 182, 182, 170, 99, 69, 69, 69, 29, 29, 9, 1, 196, 196, 196, 196, 196, 196, 196] 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, 41, 42])
total number of confs: 1023
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070916 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070916
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070916/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070916
Building REAL250005070917
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070917'
/scratch/stefan/7916153/working/building/REAL250005070917 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005070917

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070917/0 /scratch/stefan/7916153/working/building/REAL250005070917 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 26)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/26
`/scratch/stefan/7916153/working/3D/26' -> `0.mol2'
Preparing input files

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

`REAL250005070917.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070917.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070917/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070917 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H](C)[NH+](C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 6
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 13
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070917 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005070917/1 /scratch/stefan/7916153/working/building/REAL250005070917 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 27)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/27
`/scratch/stefan/7916153/working/3D/27' -> `1.mol2'
Preparing input files

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

`REAL250005070917.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005070917.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070917/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.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: REAL250005070917 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H](C)N(C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 10, 5, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [63, 31, 63, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 63, 97, 97, 97, 135, 135, 135, 140, 140, 63, 63, 63, 31, 31, 11, 1, 97, 135, 135, 135, 140, 140, 140, 140, 140, 140] 140
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: 579
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070917 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070917
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005070917/1.*
0: /scratch/stefan/7916153/working/building/REAL250005070917/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070917
Building REAL250005070918
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070918'
/scratch/stefan/7916153/working/building/REAL250005070918 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070918

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070918/0 /scratch/stefan/7916153/working/building/REAL250005070918 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 28)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/28
`/scratch/stefan/7916153/working/3D/28' -> `0.mol2'
Preparing input files

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

`REAL250005070918.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070918.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070918/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070918 none CC(C)C(CO)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 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
522  conformations in input
total number of sets (complete confs): 522
using faster count positions algorithm for large data
unique positions, atoms: [154, 132, 152, 71, 132, 170, 71, 71, 44, 20, 44, 44, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 154, 154, 154, 132, 170, 170, 510, 71, 44, 44, 44, 20, 20, 9, 1] 522
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: 1420
number of broken/clashed sets: 51
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070918 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070918
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070918/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070918
Building REAL250005070919
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070919'
/scratch/stefan/7916153/working/building/REAL250005070919 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070919

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070919/0 /scratch/stefan/7916153/working/building/REAL250005070919 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 29)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/29
`/scratch/stefan/7916153/working/3D/29' -> `0.mol2'
Preparing input files

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

`REAL250005070919.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070919.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070919/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070919 none CCOC=CC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.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', '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, 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, 6, 7]
dock color type numbers: [7, 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]
0  hydrogens need 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, 134, 134, 56, 56, 56, 44, 16, 44, 44, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 134, 134, 56, 44, 44, 44, 16, 16, 4, 1] 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])
total number of confs: 589
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070919 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070919
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070919/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070919
Building REAL250005070920
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070920'
/scratch/stefan/7916153/working/building/REAL250005070920 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL250005070920

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070920/0 /scratch/stefan/7916153/working/building/REAL250005070920 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 30)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/30
`/scratch/stefan/7916153/working/3D/30' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1CCC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005070920.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070920.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070920/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070920 none CCN1CCC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.3', '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', '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, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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, 183, 183, 183, 183, 152, 152, 152, 103, 40, 103, 101, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 196, 196, 196, 196, 196, 183, 183, 183, 183, 183, 152, 103, 103, 103, 40, 40, 10, 1] 196
rigid atoms, others: [39, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 764
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070920 none CCN1CCC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.3', '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', '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, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 7]
0  hydrogens need rotated
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 28, 28, 28, 85, 161, 161, 161, 183, 183, 183, 183, 183, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 9, 28, 28, 28, 85, 85, 161, 183] 196
rigid atoms, others: [1, 2, 3, 4, 5, 6, 27, 28, 29, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 607
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070920 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005070920/1 /scratch/stefan/7916153/working/building/REAL250005070920 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 31)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/31
`/scratch/stefan/7916153/working/3D/31' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@@H+]1CCC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005070920.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005070920.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070920/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070920 none CC[N@@H+]1CCC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 1, 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
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [44, 44, 44, 44, 44, 44, 36, 36, 36, 22, 15, 22, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 36, 22, 22, 22, 15, 15, 10, 1] 44
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: 166
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070920 none CC[N@@H+]1CCC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 1, 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
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, 1, 8, 8, 8, 18, 18, 18, 30, 31, 31, 31, 44, 44, 44, 44, 44, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 8, 18, 18, 18, 30, 30, 31, 44] 44
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 28, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 165
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070920 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `2'
/scratch/stefan/7916153/working/building/REAL250005070920/2 /scratch/stefan/7916153/working/building/REAL250005070920 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 2 (index: 32)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/32
`/scratch/stefan/7916153/working/3D/32' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@H+]1CCC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005070920.mol2' -> `2.mol2'
`temp.mol2' -> `REAL250005070920.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070920/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070920 none CC[N@H+]1CCC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 1, 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
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [83, 81, 81, 81, 81, 81, 54, 54, 54, 33, 20, 33, 33, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 81, 81, 81, 81, 81, 54, 33, 33, 33, 20, 20, 12, 1] 83
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: 297
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070920 none CC[N@H+]1CCC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 1, 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
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 29, 29, 29, 50, 52, 52, 52, 81, 81, 81, 81, 81, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 12, 29, 29, 29, 50, 50, 52, 81] 83
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 28, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 278
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070920 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070920
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
2: /scratch/stefan/7916153/working/building/REAL250005070920/2.*
1: /scratch/stefan/7916153/working/building/REAL250005070920/1.*
0: /scratch/stefan/7916153/working/building/REAL250005070920/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070920
Building REAL250005070921
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070921'
/scratch/stefan/7916153/working/building/REAL250005070921 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070921

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070921/0 /scratch/stefan/7916153/working/building/REAL250005070921 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 33)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/33
`/scratch/stefan/7916153/working/3D/33' -> `0.mol2'
Preparing input files

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

`REAL250005070921.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070921.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070921/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070921 none CCC(C)=C(C)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', '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', 'H', 'H', '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, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 149, 149, 149, 100, 149, 100, 100, 58, 16, 58, 57, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 149, 149, 149, 149, 149, 149, 100, 58, 58, 58, 16, 16, 4, 1] 201
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: 850
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070921 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070921
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070921/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070921
Building REAL250005070922
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070922'
/scratch/stefan/7916153/working/building/REAL250005070922 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070922

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070922/0 /scratch/stefan/7916153/working/building/REAL250005070922 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 34)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/34
`/scratch/stefan/7916153/working/3D/34' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CCC1)

`REAL250005070922.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070922.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070922/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070922 none COC1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CCC1 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', '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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 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, 143, 143, 143, 84, 32, 84, 82, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 200, 200, 200, 201, 201, 201, 143, 84, 84, 84, 32, 32, 9, 1, 200, 200, 200, 200, 200, 200] 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, 37, 38])
total number of confs: 716
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070922 none COC1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CCC1 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', '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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 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, 1, 1, 9, 9, 9, 35, 35, 35, 122, 189, 189, 189, 200, 200, 200, 200, 200, 1, 1, 1, 6, 6, 6, 9, 35, 35, 35, 122, 122, 189, 200, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 2, 3, 36, 37, 35, 33, 34, 19, 20, 21, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 717
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070922 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070922
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070922/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070922
Building REAL250005070923
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070923'
/scratch/stefan/7916153/working/building/REAL250005070923 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070923

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070923/0 /scratch/stefan/7916153/working/building/REAL250005070923 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 35)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/35
`/scratch/stefan/7916153/working/3D/35' -> `0.mol2'
Preparing input files

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

`REAL250005070923.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070923.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070923/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070923 none C=CCCC(=O)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.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', '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, 1, 11, 8, 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, 6, 7]
dock color type numbers: [7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 193, 79, 55, 79, 55, 55, 32, 9, 32, 32, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 193, 55, 32, 32, 32, 9, 9, 3, 1] 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])
total number of confs: 812
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070923 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070923
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070923/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070923
Building REAL250005070924
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070924'
/scratch/stefan/7916153/working/building/REAL250005070924 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070924

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070924/0 /scratch/stefan/7916153/working/building/REAL250005070924 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 36)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/36
`/scratch/stefan/7916153/working/3D/36' -> `0.mol2'
Preparing input files

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

`REAL250005070924.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070924.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070924/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070924 none CC(O)CCCC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [186, 151, 201, 110, 93, 31, 31, 31, 28, 15, 28, 28, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 142, 150, 131, 131, 93, 93, 31, 28, 28, 28, 15, 15, 4, 1] 603
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: 1752
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070924 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070924
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070924/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070924
Building REAL250005070925
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070925'
/scratch/stefan/7916153/working/building/REAL250005070925 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070925

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070925/0 /scratch/stefan/7916153/working/building/REAL250005070925 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 37)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/37
`/scratch/stefan/7916153/working/3D/37' -> `0.mol2'
Preparing input files

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

`REAL250005070925.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070925.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070925/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070925 none CC(=O)OCC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 5, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 154, 93, 93, 93, 59, 20, 59, 58, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 154, 154, 93, 59, 59, 59, 20, 20, 4, 1] 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])
total number of confs: 732
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070925 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070925
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070925/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070925
Building REAL250005070926
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070926'
/scratch/stefan/7916153/working/building/REAL250005070926 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070926

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070926/0 /scratch/stefan/7916153/working/building/REAL250005070926 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 38)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/38
`/scratch/stefan/7916153/working/3D/38' -> `0.mol2'
Preparing input files

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

`REAL250005070926.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070926.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070926/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070926 none CC(=O)NCCC(=O)N[C@H](C)CNC(=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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 6, 4, 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, 201, 201, 178, 165, 77, 77, 77, 56, 24, 56, 56, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 178, 178, 165, 165, 77, 56, 56, 56, 24, 24, 9, 1] 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])
total number of confs: 833
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070926 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070926
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070926/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070926
Building REAL250005070927
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070927'
/scratch/stefan/7916153/working/building/REAL250005070927 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070927

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070927/0 /scratch/stefan/7916153/working/building/REAL250005070927 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 39)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/39
`/scratch/stefan/7916153/working/3D/39' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNC(=O)N1)

`REAL250005070927.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070927.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070927/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070927 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 1, 11, 1, 1, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 6, 4, 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: [24, 7, 24, 24, 56, 87, 87, 87, 92, 92, 92, 92, 92, 7, 1, 7, 1, 1, 1, 1, 1, 1, 24, 24, 24, 56, 56, 87, 92, 7, 1, 1, 1] 92
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 336
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070927 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 1, 11, 1, 1, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 6, 4, 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: [50, 22, 51, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 51, 72, 72, 72, 92, 92, 92, 92, 92, 51, 51, 51, 22, 22, 10, 1, 72, 92, 92, 92] 92
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])
total number of confs: 305
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070927 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070927
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070927/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070927
Building REAL250005070928
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070928'
/scratch/stefan/7916153/working/building/REAL250005070928 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070928

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070928/0 /scratch/stefan/7916153/working/building/REAL250005070928 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 40)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/40
`/scratch/stefan/7916153/working/3D/40' -> `0.mol2'
Preparing input files

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

`REAL250005070928.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070928.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070928/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070928 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(C)[NH+](C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 7, 1, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 21
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070928 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070928
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070928/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070928
Building REAL250005070929
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070929'
/scratch/stefan/7916153/working/building/REAL250005070929 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070929

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070929/0 /scratch/stefan/7916153/working/building/REAL250005070929 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 41)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/41
`/scratch/stefan/7916153/working/3D/41' -> `0.mol2'
Preparing input files

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

`REAL250005070929.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070929.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070929/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070929 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)(F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'O.3', '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, 8, 1, 11, 5, 15, 15, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [62, 21, 63, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 63, 106, 106, 106, 197, 197, 197, 201, 63, 63, 63, 21, 21, 6, 1, 106, 201, 201, 603] 603
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])
total number of confs: 1405
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070929 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070929
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070929/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070929
Building REAL250005070930
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070930'
/scratch/stefan/7916153/working/building/REAL250005070930 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070930

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070930/0 /scratch/stefan/7916153/working/building/REAL250005070930 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 42)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/42
`/scratch/stefan/7916153/working/3D/42' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C#CC1(C)CC1)

`REAL250005070930.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070930.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070930/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070930 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C#CC1(C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', '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, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 36, 82, 82, 82, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 36, 36, 82, 85, 1, 2, 2, 2, 1, 1, 1, 1] 85
rigid atoms, others: [1, 34, 35, 36, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32])
total number of confs: 287
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070930 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C#CC1(C)CC1 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', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', '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, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [64, 27, 64, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 64, 85, 85, 85, 85, 85, 85, 85, 85, 64, 64, 64, 27, 27, 8, 1, 85, 85, 85, 85, 85, 85, 85, 85] 85
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])
total number of confs: 327
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070930 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070930
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070930/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070930
Building REAL250005070931
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070931'
/scratch/stefan/7916153/working/building/REAL250005070931 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070931

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070931/0 /scratch/stefan/7916153/working/building/REAL250005070931 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 43)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/43
`/scratch/stefan/7916153/working/3D/43' -> `0.mol2'
Preparing input files

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

`REAL250005070931.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070931.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070931/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070931 none CC(=O)C=CC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 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]
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, 95, 102, 95, 71, 71, 71, 48, 24, 48, 48, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 102, 102, 102, 95, 95, 71, 48, 48, 48, 24, 24, 10, 1] 102
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])
total number of confs: 374
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070931 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070931
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070931/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070931
Building REAL250005070932
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070932'
/scratch/stefan/7916153/working/building/REAL250005070932 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070932

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070932/0 /scratch/stefan/7916153/working/building/REAL250005070932 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 44)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/44
`/scratch/stefan/7916153/working/3D/44' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COC1CC1)

`REAL250005070932.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070932.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070932/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070932 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COC1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [121, 77, 121, 121, 166, 201, 201, 201, 201, 201, 201, 201, 201, 77, 23, 77, 6, 1, 1, 1, 1, 121, 121, 121, 166, 166, 201, 201, 77, 23, 23, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 796
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070932 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COC1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 10, 33, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 33, 59, 59, 59, 128, 171, 201, 201, 33, 33, 33, 10, 10, 4, 1, 59, 128, 128, 201, 201, 201, 201, 201] 201
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: 706
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070932 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070932
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070932/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070932
Building REAL250005070933
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070933'
/scratch/stefan/7916153/working/building/REAL250005070933 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070933

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070933/0 /scratch/stefan/7916153/working/building/REAL250005070933 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 45)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/45
`/scratch/stefan/7916153/working/3D/45' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC=CN1)

`REAL250005070933.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070933.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070933/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070933 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC=CN1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 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: [16, 4, 16, 16, 46, 86, 86, 86, 98, 98, 98, 98, 98, 4, 1, 4, 1, 1, 1, 1, 1, 16, 16, 16, 46, 46, 86, 98, 4, 1, 1, 1] 98
rigid atoms, others: [14, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 321
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070933 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC=CN1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 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: [29, 16, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 29, 32, 32, 32, 34, 34, 34, 34, 29, 29, 29, 16, 16, 7, 1, 32, 34, 34, 34] 34
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])
total number of confs: 130
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070933 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070933
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070933/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070933
Building REAL250005070934
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070934'
/scratch/stefan/7916153/working/building/REAL250005070934 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070934

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070934/0 /scratch/stefan/7916153/working/building/REAL250005070934 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 46)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/46
`/scratch/stefan/7916153/working/3D/46' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CC1CCC1)

`REAL250005070934.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070934.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070934/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070934 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CC1CCC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 41, 85, 85, 157, 201, 201, 201, 201, 201, 201, 201, 201, 41, 9, 41, 9, 1, 1, 1, 1, 1, 85, 85, 85, 157, 157, 201, 201, 41, 9, 9, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 796
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070934 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CC1CCC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 56, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 56, 82, 82, 82, 162, 162, 201, 201, 201, 56, 56, 56, 21, 21, 5, 1, 82, 162, 162, 201, 201, 201, 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, 38])
total number of confs: 710
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070934 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070934
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070934/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070934
Building REAL250005070935
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070935'
/scratch/stefan/7916153/working/building/REAL250005070935 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070935

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070935/0 /scratch/stefan/7916153/working/building/REAL250005070935 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 47)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/47
`/scratch/stefan/7916153/working/3D/47' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN=CS1)

`REAL250005070935.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070935.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070935/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070935 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN=CS1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', '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, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [22, 7, 22, 22, 62, 108, 108, 108, 112, 112, 112, 112, 112, 7, 1, 7, 1, 1, 1, 1, 1, 22, 22, 22, 62, 62, 108, 112, 7, 1] 112
rigid atoms, others: [14, 16, 17, 18, 19, 20, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 395
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070935 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN=CS1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', '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, 8, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [67, 30, 68, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 68, 104, 104, 104, 112, 112, 112, 112, 68, 68, 68, 30, 30, 9, 1, 104, 112] 112
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])
total number of confs: 408
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070935 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070935
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070935/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070935
Building REAL250005070936
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070936'
/scratch/stefan/7916153/working/building/REAL250005070936 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070936

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070936/0 /scratch/stefan/7916153/working/building/REAL250005070936 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 48)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/48
`/scratch/stefan/7916153/working/3D/48' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(=O)CO1)

`REAL250005070936.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070936.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070936/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070936 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(=O)CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', '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, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 11, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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
181  conformations in input
total number of sets (complete confs): 181
using faster count positions algorithm for large data
unique positions, atoms: [36, 11, 36, 36, 111, 172, 172, 172, 181, 181, 181, 181, 181, 11, 1, 11, 1, 1, 1, 1, 1, 1, 36, 36, 36, 111, 111, 172, 181, 11, 1, 1, 1, 1, 1] 181
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 644
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070936 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(=O)CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', '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, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 11, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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
181  conformations in input
total number of sets (complete confs): 181
using faster count positions algorithm for large data
unique positions, atoms: [87, 32, 88, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 88, 134, 134, 134, 181, 181, 181, 181, 181, 88, 88, 88, 32, 32, 10, 1, 134, 181, 181, 181, 181, 181] 181
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])
total number of confs: 668
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070936 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070936
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070936/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070936
Building REAL250005070937
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070937'
/scratch/stefan/7916153/working/building/REAL250005070937 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070937

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070937/0 /scratch/stefan/7916153/working/building/REAL250005070937 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 49)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/49
`/scratch/stefan/7916153/working/3D/49' -> `0.mol2'
Preparing input files

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

`REAL250005070937.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070937.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070937/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070937 none CC(C)NC(=O)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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', 'H', 'H', '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, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 197, 201, 197, 150, 197, 150, 150, 85, 29, 85, 83, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 197, 150, 85, 85, 85, 29, 29, 10, 1] 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])
total number of confs: 720
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070937 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070937
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070937/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070937
Building REAL250005070938
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070938'
/scratch/stefan/7916153/working/building/REAL250005070938 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070938

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070938/0 /scratch/stefan/7916153/working/building/REAL250005070938 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 50)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/50
`/scratch/stefan/7916153/working/3D/50' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CCO1)

`REAL250005070938.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070938.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070938/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070938 none CC1=C(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CCO1 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', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 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]
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, 118, 118, 118, 74, 30, 74, 72, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 188, 188, 188, 188, 188, 188, 118, 74, 74, 74, 30, 30, 10, 1, 188, 188, 188, 188] 188
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: 551
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070938 none CC1=C(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CCO1 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', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 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]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 40, 40, 40, 118, 177, 177, 177, 188, 188, 188, 188, 188, 1, 1, 1, 2, 2, 2, 9, 40, 40, 40, 118, 118, 177, 188, 1, 1, 1, 1] 188
rigid atoms, others: [0, 1, 2, 3, 36, 35, 33, 34, 19, 20, 21] 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, 31, 32])
total number of confs: 675
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070938 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070938
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070938/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070938
Building REAL250005070939
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070939'
/scratch/stefan/7916153/working/building/REAL250005070939 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070939

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070939/0 /scratch/stefan/7916153/working/building/REAL250005070939 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 51)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/51
`/scratch/stefan/7916153/working/3D/51' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC=CN1C)

`REAL250005070939.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070939.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070939/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070939 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC=CN1C 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', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [17, 4, 17, 17, 54, 104, 104, 104, 111, 111, 111, 111, 111, 4, 1, 4, 1, 1, 1, 1, 1, 1, 17, 17, 17, 54, 54, 104, 111, 4, 1, 1, 2, 2, 2] 111
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 30, 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, 32, 33, 34])
total number of confs: 387
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070939 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NC=CN1C 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', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [79, 32, 80, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 80, 109, 109, 109, 111, 111, 111, 111, 111, 80, 80, 80, 32, 32, 9, 1, 109, 111, 111, 111, 111, 111] 111
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])
total number of confs: 419
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070939 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070939
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070939/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070939
Building REAL250005070940
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070940'
/scratch/stefan/7916153/working/building/REAL250005070940 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070940

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070940/0 /scratch/stefan/7916153/working/building/REAL250005070940 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 52)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/52
`/scratch/stefan/7916153/working/3D/52' -> `0.mol2'
Preparing input files

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

`REAL250005070940.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070940.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070940/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070940 none CC(CO)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 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', '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, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [192, 108, 192, 201, 108, 108, 69, 23, 69, 67, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 201, 201, 603, 108, 69, 69, 69, 23, 23, 7, 1] 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])
total number of confs: 1452
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070940 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070940
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070940/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070940
Building REAL250005070941
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070941'
/scratch/stefan/7916153/working/building/REAL250005070941 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070941

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070941/0 /scratch/stefan/7916153/working/building/REAL250005070941 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 53)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/53
`/scratch/stefan/7916153/working/3D/53' -> `0.mol2'
Preparing input files

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

`REAL250005070941.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070941.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070941/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070941 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CON=C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [21, 5, 21, 21, 78, 124, 124, 124, 134, 134, 134, 134, 134, 5, 1, 5, 1, 1, 1, 1, 1, 21, 21, 21, 78, 78, 124, 134, 5, 1, 1] 134
rigid atoms, others: [14, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 483
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070941 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CON=C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [50, 21, 51, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 51, 77, 77, 77, 134, 134, 134, 134, 51, 51, 51, 21, 21, 10, 1, 77, 134, 134] 134
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])
total number of confs: 405
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070941 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070941
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070941/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070941
Building REAL250005070942
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070942'
/scratch/stefan/7916153/working/building/REAL250005070942 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070942

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070942/0 /scratch/stefan/7916153/working/building/REAL250005070942 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 54)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/54
`/scratch/stefan/7916153/working/3D/54' -> `0.mol2'
Preparing input files

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

`REAL250005070942.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070942.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070942/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070942 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCCO 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [38, 18, 38, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 38, 47, 47, 47, 143, 173, 198, 200, 38, 38, 38, 18, 18, 5, 1, 47, 143, 143, 185, 185, 197, 199, 201, 201, 600] 603
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, 36, 37])
total number of confs: 1549
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070942 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070942
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070942/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070942
Building REAL250005070943
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070943'
/scratch/stefan/7916153/working/building/REAL250005070943 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070943

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070943/0 /scratch/stefan/7916153/working/building/REAL250005070943 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 55)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/55
`/scratch/stefan/7916153/working/3D/55' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(=O)C1CC1)

`REAL250005070943.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070943.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070943/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070943 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [88, 48, 88, 88, 149, 201, 201, 201, 201, 201, 201, 201, 201, 48, 12, 48, 1, 12, 1, 1, 1, 88, 88, 88, 149, 149, 201, 201, 48, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 16, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 759
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070943 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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, 14, 52, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 52, 101, 101, 101, 156, 156, 201, 201, 52, 52, 52, 14, 14, 4, 1, 101, 201, 201, 201, 201, 201] 201
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])
total number of confs: 719
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070943 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070943
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070943/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070943
Building REAL250005070944
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070944'
/scratch/stefan/7916153/working/building/REAL250005070944 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070944

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070944/0 /scratch/stefan/7916153/working/building/REAL250005070944 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 56)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/56
`/scratch/stefan/7916153/working/3D/56' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1COC(=O)N1)

`REAL250005070944.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070944.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070944/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070944 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1COC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 6, 4, 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: [30, 10, 30, 30, 84, 111, 111, 111, 120, 120, 120, 120, 120, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 84, 84, 111, 120, 10, 1, 1, 1] 120
rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 445
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070944 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1COC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 6, 4, 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: [68, 28, 68, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 68, 100, 100, 100, 120, 120, 120, 120, 120, 120, 68, 68, 68, 28, 28, 8, 1, 100, 120, 120, 120] 120
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 435
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070944 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070944
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070944/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070944
Building REAL250005070945
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070945'
/scratch/stefan/7916153/working/building/REAL250005070945 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070945

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070945/0 /scratch/stefan/7916153/working/building/REAL250005070945 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 57)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/57
`/scratch/stefan/7916153/working/3D/57' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(O)CC1)

`REAL250005070945.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070945.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070945/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070945 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(O)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 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: [72, 29, 72, 72, 136, 171, 171, 171, 176, 176, 176, 176, 176, 29, 7, 29, 1, 1, 1, 1, 1, 72, 72, 72, 136, 136, 171, 176, 29, 7, 7, 6, 1, 1, 1, 1] 528
rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 706
number of broken/clashed sets: 46
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070945 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(O)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 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: [64, 23, 64, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 64, 92, 92, 92, 159, 176, 176, 176, 64, 64, 64, 23, 23, 8, 1, 92, 159, 159, 528, 176, 176, 176, 176] 528
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: 1252
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070945 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070945
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070945/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070945
Building REAL250005070946
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070946'
/scratch/stefan/7916153/working/building/REAL250005070946 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070946

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070946/0 /scratch/stefan/7916153/working/building/REAL250005070946 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 58)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/58
`/scratch/stefan/7916153/working/3D/58' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC1F)

`REAL250005070946.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070946.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070946/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070946 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC1F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [47, 13, 47, 47, 130, 174, 174, 174, 183, 183, 183, 183, 183, 13, 1, 13, 1, 1, 1, 1, 1, 47, 47, 47, 130, 130, 174, 183, 13, 1, 1, 1, 1, 1, 1] 183
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 678
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070946 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC1F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [70, 29, 72, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 72, 114, 114, 114, 183, 183, 183, 183, 72, 72, 72, 29, 29, 10, 1, 114, 183, 183, 183, 183, 183, 183] 183
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])
total number of confs: 640
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070946 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070946
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070946/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070946
Building REAL250005070947
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070947'
/scratch/stefan/7916153/working/building/REAL250005070947 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070947

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070947/0 /scratch/stefan/7916153/working/building/REAL250005070947 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 59)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/59
`/scratch/stefan/7916153/working/3D/59' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)C1CCC1)

`REAL250005070947.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070947.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070947/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070947 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)C1CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 33, 78, 78, 157, 201, 201, 201, 201, 201, 201, 201, 201, 33, 6, 33, 1, 6, 1, 1, 1, 1, 78, 78, 78, 157, 157, 201, 201, 33, 6, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 16, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 796
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070947 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)C1CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 62, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 62, 111, 111, 111, 151, 151, 201, 201, 201, 62, 62, 62, 19, 19, 5, 1, 111, 151, 201, 201, 201, 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: 797
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070947 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070947
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070947/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070947
Building REAL250005070948
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070948'
/scratch/stefan/7916153/working/building/REAL250005070948 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070948

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070948/0 /scratch/stefan/7916153/working/building/REAL250005070948 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 60)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/60
`/scratch/stefan/7916153/working/3D/60' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(C)O1)

`REAL250005070948.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070948.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070948/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070948 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(C)O1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [8, 3, 8, 8, 37, 70, 70, 70, 77, 77, 77, 77, 77, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 37, 37, 70, 77, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2] 77
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21, 30, 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, 33, 34, 35, 36, 37, 38])
total number of confs: 265
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070948 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(C)O1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [56, 29, 57, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 57, 75, 75, 75, 77, 77, 77, 77, 77, 57, 57, 57, 29, 29, 8, 1, 75, 77, 77, 77, 77, 77, 77, 77, 77, 77] 77
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: 307
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070948 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070948
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070948/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070948
Building REAL250005070949
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070949'
/scratch/stefan/7916153/working/building/REAL250005070949 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070949

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070949/0 /scratch/stefan/7916153/working/building/REAL250005070949 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 61)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/61
`/scratch/stefan/7916153/working/3D/61' -> `0.mol2'
Preparing input files

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

`REAL250005070949.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070949.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070949/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070949 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@H]1CF 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 12, 38, 38, 108, 173, 173, 173, 195, 195, 195, 195, 195, 12, 1, 12, 1, 1, 1, 1, 1, 1, 9, 38, 38, 38, 108, 108, 173, 195, 12, 1, 1, 9, 9] 201
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 704
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070949 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@H]1CF 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 64, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 64, 94, 94, 94, 195, 195, 195, 195, 195, 201, 64, 64, 64, 23, 23, 10, 1, 94, 195, 195, 201, 201] 201
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 659
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070949 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070949
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070949/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070949
Building REAL250005070950
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070950'
/scratch/stefan/7916153/working/building/REAL250005070950 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070950

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070950/0 /scratch/stefan/7916153/working/building/REAL250005070950 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 62)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/62
`/scratch/stefan/7916153/working/3D/62' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)=C1CCC1)

`REAL250005070950.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070950.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070950/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070950 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)=C1CCC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [30, 9, 30, 30, 80, 132, 132, 132, 143, 143, 143, 143, 143, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 30, 30, 80, 80, 132, 143, 9, 1, 1, 1, 1, 1, 1] 143
rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 504
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070950 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)=C1CCC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [78, 33, 79, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 79, 119, 119, 119, 143, 143, 143, 143, 143, 79, 79, 79, 33, 33, 9, 1, 119, 143, 143, 143, 143, 143, 143] 143
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: 523
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070950 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070950
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070950/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070950
Building REAL250005070951
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070951'
/scratch/stefan/7916153/working/building/REAL250005070951 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070951

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070951/0 /scratch/stefan/7916153/working/building/REAL250005070951 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 63)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/63
`/scratch/stefan/7916153/working/3D/63' -> `0.mol2'
Preparing input files

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

`REAL250005070951.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070951.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070951/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070951 none CCC(CO)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 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
567  conformations in input
total number of sets (complete confs): 567
using faster count positions algorithm for large data
unique positions, atoms: [157, 143, 72, 143, 181, 72, 72, 47, 23, 47, 47, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 167, 143, 181, 181, 543, 72, 47, 47, 47, 23, 23, 9, 1] 567
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: 1543
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070951 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070951
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070951/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070951
Building REAL250005070952
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070952'
/scratch/stefan/7916153/working/building/REAL250005070952 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070952

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070952/0 /scratch/stefan/7916153/working/building/REAL250005070952 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 64)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/64
`/scratch/stefan/7916153/working/3D/64' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(O)C1CC1)

`REAL250005070952.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070952.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070952/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070952 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
396  conformations in input
total number of sets (complete confs): 396
using faster count positions algorithm for large data
unique positions, atoms: [89, 61, 89, 89, 127, 131, 131, 131, 132, 132, 132, 132, 132, 61, 21, 61, 4, 1, 4, 1, 1, 1, 89, 89, 89, 127, 127, 131, 132, 61, 21, 21, 4, 12, 1, 1, 1, 1, 1] 396
rigid atoms, others: [34, 35, 36, 37, 38, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 541
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070952 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
396  conformations in input
total number of sets (complete confs): 396
using faster count positions algorithm for large data
unique positions, atoms: [20, 10, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 20, 33, 33, 33, 81, 112, 112, 132, 132, 20, 20, 20, 10, 10, 4, 1, 33, 81, 81, 112, 336, 132, 132, 132, 132, 132] 396
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: 893
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070952 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070952
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070952/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070952
Building REAL250005070953
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070953'
/scratch/stefan/7916153/working/building/REAL250005070953 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070953

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070953/0 /scratch/stefan/7916153/working/building/REAL250005070953 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 65)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/65
`/scratch/stefan/7916153/working/3D/65' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=CC1CC1)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005070953.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070953.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070953/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070953 none CC(=CC1CC1)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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: [140, 67, 140, 140, 201, 201, 67, 67, 48, 17, 48, 48, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 201, 201, 201, 201, 201, 67, 48, 48, 48, 17, 17, 4, 1] 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])
total number of confs: 709
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070953 none CC(=CC1CC1)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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: [5, 5, 1, 1, 1, 1, 5, 30, 30, 30, 72, 72, 72, 146, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 6, 5, 1, 1, 1, 1, 1, 30, 72, 72, 72, 146, 146, 201, 201] 201
rigid atoms, others: [2, 3, 4, 5, 26, 27, 28, 29, 30] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 767
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070953 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070953
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070953/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070953
Building REAL250005070954
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070954'
/scratch/stefan/7916153/working/building/REAL250005070954 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070954

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070954/0 /scratch/stefan/7916153/working/building/REAL250005070954 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 66)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/66
`/scratch/stefan/7916153/working/3D/66' -> `0.mol2'
Preparing input files

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

`REAL250005070954.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070954.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070954/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070954 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@@H]1C#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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [23, 8, 23, 23, 56, 78, 78, 78, 85, 85, 85, 85, 85, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 56, 56, 78, 85, 8, 1, 1] 85
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 308
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070954 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@@H]1C#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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [49, 20, 50, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 50, 76, 76, 76, 85, 85, 85, 85, 85, 85, 50, 50, 50, 20, 20, 9, 1, 76, 85, 85] 85
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32])
total number of confs: 320
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070954 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070954
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070954/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070954
Building REAL250005070955
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070955'
/scratch/stefan/7916153/working/building/REAL250005070955 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070955

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070955/0 /scratch/stefan/7916153/working/building/REAL250005070955 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 67)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/67
`/scratch/stefan/7916153/working/3D/67' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CN=CO1)

`REAL250005070955.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070955.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070955/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070955 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CN=CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 34, 72, 72, 150, 201, 201, 201, 201, 201, 201, 201, 201, 34, 5, 34, 1, 1, 1, 1, 1, 1, 72, 72, 72, 150, 150, 201, 201, 34, 5, 5, 1, 1] 201
rigid atoms, others: [32, 33, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 807
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070955 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CN=CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 15, 37, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 37, 54, 54, 54, 122, 201, 201, 201, 201, 37, 37, 37, 15, 15, 4, 1, 54, 122, 122, 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])
total number of confs: 613
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070955 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070955
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070955/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070955
Building REAL250005070956
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070956'
/scratch/stefan/7916153/working/building/REAL250005070956 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070956

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070956/0 /scratch/stefan/7916153/working/building/REAL250005070956 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 68)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/68
`/scratch/stefan/7916153/working/3D/68' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COCC1)

`REAL250005070956.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070956.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070956/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070956 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COCC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
133  conformations in input
total number of sets (complete confs): 133
using faster count positions algorithm for large data
unique positions, atoms: [38, 11, 38, 38, 96, 128, 128, 128, 133, 133, 133, 133, 133, 11, 1, 11, 1, 1, 1, 1, 1, 38, 38, 38, 96, 96, 128, 133, 11, 1, 1, 1, 1, 1] 133
rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 506
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070956 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=COCC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
133  conformations in input
total number of sets (complete confs): 133
using faster count positions algorithm for large data
unique positions, atoms: [67, 28, 69, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 69, 102, 102, 102, 133, 133, 133, 133, 69, 69, 69, 28, 28, 10, 1, 102, 133, 133, 133, 133, 133] 133
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])
total number of confs: 439
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070956 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070956
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070956/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070956
Building REAL250005070957
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070957'
/scratch/stefan/7916153/working/building/REAL250005070957 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070957

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070957/0 /scratch/stefan/7916153/working/building/REAL250005070957 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 69)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/69
`/scratch/stefan/7916153/working/3D/69' -> `0.mol2'
Preparing input files

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

`REAL250005070957.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070957.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070957/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070957 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC(C)(C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [45, 16, 45, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 45, 65, 65, 65, 164, 165, 201, 201, 200, 45, 45, 45, 16, 16, 4, 1, 65, 164, 164, 166, 166, 201, 201, 201, 201, 201, 201, 603] 603
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, 39, 40])
total number of confs: 1492
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070957 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070957
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070957/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070957
Building REAL250005070958
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070958'
/scratch/stefan/7916153/working/building/REAL250005070958 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070958

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070958/0 /scratch/stefan/7916153/working/building/REAL250005070958 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 70)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/70
`/scratch/stefan/7916153/working/3D/70' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)N1)

`REAL250005070958.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070958.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070958/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070958 none CC1=CC=C(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 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, 102, 102, 102, 85, 85, 85, 64, 27, 64, 63, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 102, 102, 85, 64, 64, 64, 27, 27, 9, 1, 102] 102
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])
total number of confs: 355
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070958 none CC1=CC=C(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.pl3', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 23, 23, 23, 62, 95, 95, 95, 102, 102, 102, 102, 102, 1, 2, 2, 2, 1, 1, 8, 23, 23, 23, 62, 62, 95, 102, 1] 102
rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 377
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070958 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070958
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070958/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070958
Building REAL250005070959
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070959'
/scratch/stefan/7916153/working/building/REAL250005070959 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070959

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070959/0 /scratch/stefan/7916153/working/building/REAL250005070959 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 71)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/71
`/scratch/stefan/7916153/working/3D/71' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CC1)

`REAL250005070959.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070959.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070959/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070959 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
429  conformations in input
total number of sets (complete confs): 429
using faster count positions algorithm for large data
unique positions, atoms: [38, 11, 38, 38, 97, 137, 137, 137, 143, 143, 143, 143, 143, 11, 1, 11, 1, 1, 1, 1, 38, 38, 38, 97, 97, 137, 143, 11, 6, 1, 1, 1, 1] 429
rigid atoms, others: [32, 14, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 524
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070959 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
429  conformations in input
total number of sets (complete confs): 429
using faster count positions algorithm for large data
unique positions, atoms: [70, 31, 72, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 72, 97, 97, 97, 143, 143, 143, 72, 72, 72, 31, 31, 8, 1, 97, 429, 143, 143, 143, 143] 429
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32])
total number of confs: 943
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070959 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070959
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070959/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070959
Building REAL250005070960
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070960'
/scratch/stefan/7916153/working/building/REAL250005070960 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070960

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070960/0 /scratch/stefan/7916153/working/building/REAL250005070960 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 72)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/72
`/scratch/stefan/7916153/working/3D/72' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCC1)

`REAL250005070960.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070960.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070960/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070960 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [17, 6, 17, 17, 44, 60, 60, 60, 62, 62, 62, 62, 62, 6, 1, 6, 1, 1, 1, 1, 17, 17, 17, 44, 44, 60, 62, 6, 1, 1, 1, 1, 1] 62
rigid atoms, others: [32, 14, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 225
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070960 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [52, 22, 52, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 52, 62, 62, 62, 62, 62, 62, 52, 52, 52, 22, 22, 9, 1, 62, 62, 62, 62, 62, 62] 62
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32])
total number of confs: 233
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070960 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070960
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070960/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070960
Building REAL250005070961
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070961'
/scratch/stefan/7916153/working/building/REAL250005070961 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070961

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070961/0 /scratch/stefan/7916153/working/building/REAL250005070961 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 73)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/73
`/scratch/stefan/7916153/working/3D/73' -> `0.mol2'
Preparing input files

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

`REAL250005070961.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070961.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070961/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070961 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NOC(C)C1 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', 'N.am', 'C.2', 'O.2', 'C.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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [36, 13, 36, 36, 92, 134, 134, 134, 137, 137, 137, 137, 137, 13, 1, 13, 1, 1, 1, 1, 1, 1, 36, 36, 36, 92, 92, 134, 137, 13, 1, 2, 2, 2, 1, 1] 137
rigid atoms, others: [34, 35, 14, 16, 17, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33])
total number of confs: 509
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070961 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NOC(C)C1 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', 'N.am', 'C.2', 'O.2', 'C.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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [79, 32, 80, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 80, 129, 129, 129, 137, 137, 137, 137, 137, 80, 80, 80, 32, 32, 9, 1, 129, 137, 137, 137, 137, 137, 137] 137
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: 484
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070961 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070961
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070961/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070961
Building REAL250005070962
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070962'
/scratch/stefan/7916153/working/building/REAL250005070962 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070962

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070962/0 /scratch/stefan/7916153/working/building/REAL250005070962 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 74)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/74
`/scratch/stefan/7916153/working/3D/74' -> `0.mol2'
Preparing input files

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

`REAL250005070962.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070962.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070962/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070962 none CC(CF)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 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', '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, 15, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 113, 197, 201, 113, 113, 67, 22, 67, 65, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 201, 201, 113, 67, 67, 67, 22, 22, 7, 1] 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])
total number of confs: 824
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070962 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070962
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070962/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070962
Building REAL250005070963
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070963'
/scratch/stefan/7916153/working/building/REAL250005070963 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070963

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070963/0 /scratch/stefan/7916153/working/building/REAL250005070963 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 75)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/75
`/scratch/stefan/7916153/working/3D/75' -> `0.mol2'
Preparing input files

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

`REAL250005070963.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070963.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070963/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070963 none CC(Cl)=CC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'Cl', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 16, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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]
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, 98, 98, 98, 68, 31, 68, 68, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 98, 68, 68, 68, 31, 31, 11, 1] 136
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])
total number of confs: 492
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070963 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070963
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070963/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070963
Building REAL250005070964
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070964'
/scratch/stefan/7916153/working/building/REAL250005070964 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070964

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070964/0 /scratch/stefan/7916153/working/building/REAL250005070964 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 76)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/76
`/scratch/stefan/7916153/working/3D/76' -> `0.mol2'
Preparing input files

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

`REAL250005070964.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070964.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070964/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070964 none CC=CC(=O)N[C@H](C)CNC(=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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [114, 114, 96, 96, 96, 70, 31, 70, 69, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 114, 96, 70, 70, 70, 31, 31, 10, 1] 114
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])
total number of confs: 435
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070964 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070964
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070964/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070964
Building REAL250005070965
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070965'
/scratch/stefan/7916153/working/building/REAL250005070965 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070965

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070965/0 /scratch/stefan/7916153/working/building/REAL250005070965 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 77)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/77
`/scratch/stefan/7916153/working/3D/77' -> `0.mol2'
Preparing input files

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

`REAL250005070965.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070965.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070965/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070965 none CCC(F)(F)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 15, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [186, 186, 91, 186, 186, 91, 91, 52, 19, 52, 51, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 91, 52, 52, 52, 19, 19, 6, 1] 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])
total number of confs: 938
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070965 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070965
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070965/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070965
Building REAL250005070966
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070966'
/scratch/stefan/7916153/working/building/REAL250005070966 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070966

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070966/0 /scratch/stefan/7916153/working/building/REAL250005070966 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 78)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/78
`/scratch/stefan/7916153/working/3D/78' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC1F)

`REAL250005070966.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070966.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070966/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070966 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC1F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [26, 6, 26, 26, 96, 156, 156, 156, 162, 162, 162, 162, 162, 6, 1, 6, 1, 1, 1, 1, 1, 26, 26, 26, 96, 96, 156, 162, 6, 2, 2, 2, 1, 1, 1] 162
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 582
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070966 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC1F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [76, 31, 78, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 78, 116, 116, 116, 162, 162, 162, 162, 78, 78, 78, 31, 31, 10, 1, 116, 162, 162, 162, 162, 162, 162] 162
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])
total number of confs: 584
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070966 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070966
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070966/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070966
Building REAL250005070967
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070967'
/scratch/stefan/7916153/working/building/REAL250005070967 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070967

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070967/0 /scratch/stefan/7916153/working/building/REAL250005070967 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 79)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/79
`/scratch/stefan/7916153/working/3D/79' -> `0.mol2'
Preparing input files

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

`REAL250005070967.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070967.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070967/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070967 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC(=O)O1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [35, 10, 35, 35, 81, 109, 109, 109, 113, 113, 113, 113, 113, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 81, 81, 109, 113, 10, 1, 1, 1, 1] 113
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 427
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070967 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC(=O)O1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 5, 3, 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: [56, 19, 58, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 58, 85, 85, 85, 113, 113, 113, 113, 113, 113, 58, 58, 58, 18, 18, 7, 1, 85, 113, 113, 113, 113] 113
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 409
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070967 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070967
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070967/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070967
Building REAL250005070968
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070968'
/scratch/stefan/7916153/working/building/REAL250005070968 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070968

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070968/0 /scratch/stefan/7916153/working/building/REAL250005070968 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 80)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/80
`/scratch/stefan/7916153/working/3D/80' -> `0.mol2'
Preparing input files

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

`REAL250005070968.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070968.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070968/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070968 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [61, 31, 61, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 61, 91, 91, 91, 122, 122, 136, 61, 61, 61, 31, 31, 10, 1, 91, 122, 122, 136, 136] 136
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 543
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070968 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070968
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070968/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070968
Building REAL250005070969
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070969'
/scratch/stefan/7916153/working/building/REAL250005070969 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070969

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070969/0 /scratch/stefan/7916153/working/building/REAL250005070969 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 81)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/81
`/scratch/stefan/7916153/working/3D/81' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)CC1CC1)

`REAL250005070969.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070969.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070969/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070969 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)CC1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [105, 62, 105, 105, 160, 201, 201, 201, 201, 201, 201, 201, 201, 62, 13, 62, 3, 13, 1, 1, 1, 1, 105, 105, 105, 160, 160, 201, 201, 62, 13, 3, 3, 1, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 820
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070969 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)CC1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 12, 34, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 34, 57, 57, 57, 124, 124, 163, 201, 201, 34, 34, 34, 12, 12, 4, 1, 57, 124, 163, 163, 201, 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: 859
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070969 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070969
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070969/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070969
Building REAL250005070970
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070970'
/scratch/stefan/7916153/working/building/REAL250005070970 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070970

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070970/0 /scratch/stefan/7916153/working/building/REAL250005070970 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 82)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/82
`/scratch/stefan/7916153/working/3D/82' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1COC(=O)N1)

`REAL250005070970.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070970.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070970/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070970 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1COC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  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: [24, 10, 24, 24, 54, 80, 80, 80, 84, 84, 84, 84, 84, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 54, 54, 80, 84, 10, 1, 1, 1] 84
rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 307
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070970 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1COC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  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: [50, 23, 52, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 52, 69, 69, 69, 84, 84, 84, 84, 84, 84, 52, 52, 52, 22, 22, 8, 1, 69, 84, 84, 84] 84
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 306
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070970 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070970
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070970/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070970
Building REAL250005070971
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070971'
/scratch/stefan/7916153/working/building/REAL250005070971 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070971

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070971/0 /scratch/stefan/7916153/working/building/REAL250005070971 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 83)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/83
`/scratch/stefan/7916153/working/3D/83' -> `0.mol2'
Preparing input files

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

`REAL250005070971.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070971.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070971/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070971 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCCC#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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 35, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 35, 45, 45, 45, 118, 141, 157, 198, 198, 35, 35, 35, 18, 18, 7, 1, 45, 118, 118, 150, 150, 158, 159, 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: 972
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070971 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070971
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070971/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070971
Building REAL250005070972
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070972'
/scratch/stefan/7916153/working/building/REAL250005070972 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070972

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070972/0 /scratch/stefan/7916153/working/building/REAL250005070972 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 84)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/84
`/scratch/stefan/7916153/working/3D/84' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CO)CC1)

`REAL250005070972.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070972.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070972/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070972 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CO)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [26, 7, 26, 26, 87, 181, 182, 181, 190, 190, 190, 190, 190, 7, 1, 7, 1, 1, 9, 1, 1, 26, 26, 26, 87, 87, 182, 190, 7, 9, 9, 27, 1, 1, 1, 1] 603
rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 683
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070972 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CO)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens 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, 18, 57, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 57, 101, 101, 101, 190, 201, 190, 190, 57, 57, 57, 18, 18, 6, 1, 101, 201, 201, 603, 190, 190, 190, 190] 603
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: 1309
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070972 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070972
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070972/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070972
Building REAL250005070973
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070973'
/scratch/stefan/7916153/working/building/REAL250005070973 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070973

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070973/0 /scratch/stefan/7916153/working/building/REAL250005070973 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 85)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/85
`/scratch/stefan/7916153/working/3D/85' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=NO1)

`REAL250005070973.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070973.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070973/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070973 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=NO1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 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: [21, 7, 21, 21, 55, 85, 85, 85, 87, 87, 87, 87, 87, 7, 1, 7, 1, 1, 1, 1, 1, 21, 21, 21, 55, 55, 85, 87, 7, 1, 1] 87
rigid atoms, others: [14, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 315
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070973 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=NO1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 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: [58, 22, 60, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 60, 81, 81, 81, 87, 87, 87, 87, 60, 60, 60, 22, 22, 8, 1, 81, 87, 87] 87
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])
total number of confs: 319
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070973 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070973
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070973/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070973
Building REAL250005070974
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070974'
/scratch/stefan/7916153/working/building/REAL250005070974 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL250005070974 as failed and skipping
/scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `/scratch/stefan/7916153/failed'
`/scratch/stefan/7916153/working/building/REAL250005070974' -> `/scratch/stefan/7916153/failed/REAL250005070974'
Building REAL250005070975
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070975'
/scratch/stefan/7916153/working/building/REAL250005070975 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070975

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070975/0 /scratch/stefan/7916153/working/building/REAL250005070975 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 86)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/86
`/scratch/stefan/7916153/working/3D/86' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(=O)N1)

`REAL250005070975.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070975.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070975/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070975 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [30, 9, 30, 30, 86, 127, 127, 127, 135, 135, 135, 135, 135, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 30, 30, 86, 86, 127, 135, 9, 1, 1, 1, 1, 1, 1] 135
rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 501
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070975 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [68, 25, 69, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 108, 108, 108, 135, 135, 135, 135, 135, 69, 69, 69, 25, 25, 9, 1, 108, 135, 135, 135, 135, 135, 135] 135
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: 481
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070975 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070975
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070975/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070975
Building REAL250005070976
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070976'
/scratch/stefan/7916153/working/building/REAL250005070976 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070976

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070976/0 /scratch/stefan/7916153/working/building/REAL250005070976 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 87)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/87
`/scratch/stefan/7916153/working/3D/87' -> `0.mol2'
Preparing input files

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

`REAL250005070976.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070976.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070976/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070976 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](C)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', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 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: [74, 34, 76, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 76, 107, 107, 107, 113, 113, 113, 76, 76, 76, 34, 34, 10, 1, 107, 113, 113, 113, 339] 339
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 782
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070976 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070976
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070976/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070976
Building REAL250005070977
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070977'
/scratch/stefan/7916153/working/building/REAL250005070977 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070977

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070977/0 /scratch/stefan/7916153/working/building/REAL250005070977 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 88)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/88
`/scratch/stefan/7916153/working/3D/88' -> `0.mol2'
Preparing input files

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

`REAL250005070977.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070977.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070977/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070977 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=C(F)O1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 15, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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: [21, 7, 21, 21, 62, 108, 108, 108, 115, 115, 115, 115, 115, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 62, 62, 108, 115, 7, 1, 1] 115
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 399
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070977 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC=C(F)O1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 1, 15, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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: [72, 35, 73, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 73, 110, 110, 110, 115, 115, 115, 115, 115, 73, 73, 73, 35, 35, 9, 1, 110, 115, 115] 115
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])
total number of confs: 424
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070977 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070977
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070977/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070977
Building REAL250005070978
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070978'
/scratch/stefan/7916153/working/building/REAL250005070978 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070978

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070978/0 /scratch/stefan/7916153/working/building/REAL250005070978 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 89)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/89
`/scratch/stefan/7916153/working/3D/89' -> `0.mol2'
Preparing input files

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

`REAL250005070978.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070978.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070978/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070978 none CON=CC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 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', '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, 12, 8, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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]
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, 122, 122, 122, 85, 32, 85, 83, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 122, 85, 85, 85, 32, 32, 8, 1] 146
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])
total number of confs: 553
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070978 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070978
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070978/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070978
Building REAL250005070979
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070979'
/scratch/stefan/7916153/working/building/REAL250005070979 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070979

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070979/0 /scratch/stefan/7916153/working/building/REAL250005070979 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 90)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/90
`/scratch/stefan/7916153/working/3D/90' -> `0.mol2'
Preparing input files

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

`REAL250005070979.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070979.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070979/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070979 none C#CCC(C)(C)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 153, 80, 153, 153, 80, 80, 51, 16, 51, 50, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 153, 153, 153, 153, 153, 153, 80, 51, 51, 51, 16, 16, 4, 1] 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])
total number of confs: 885
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070979 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070979
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070979/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070979
Building REAL250005070980
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070980'
/scratch/stefan/7916153/working/building/REAL250005070980 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070980

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070980/0 /scratch/stefan/7916153/working/building/REAL250005070980 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 91)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/91
`/scratch/stefan/7916153/working/3D/91' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(F)C1)

`REAL250005070980.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070980.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070980/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070980 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(F)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 47, 47, 134, 193, 193, 193, 201, 201, 201, 201, 201, 11, 1, 11, 1, 1, 1, 1, 1, 1, 47, 47, 47, 134, 134, 193, 201, 11, 1, 1, 1, 2, 2, 2, 1, 1] 201
rigid atoms, others: [32, 36, 37, 14, 16, 17, 18, 19, 20, 21, 30, 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, 33, 34, 35])
total number of confs: 734
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070980 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(F)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 80, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 80, 120, 120, 120, 201, 201, 201, 201, 201, 80, 80, 80, 28, 28, 9, 1, 120, 201, 201, 201, 201, 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: 717
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070980 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070980
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070980/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070980
Building REAL250005070981
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070981'
/scratch/stefan/7916153/working/building/REAL250005070981 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070981

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070981/0 /scratch/stefan/7916153/working/building/REAL250005070981 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 92)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/92
`/scratch/stefan/7916153/working/3D/92' -> `0.mol2'
Preparing input files

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

`REAL250005070981.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070981.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070981/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070981 none CCC(C)(OC)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 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: [190, 183, 104, 183, 183, 189, 104, 104, 59, 18, 59, 57, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 183, 183, 183, 189, 189, 189, 104, 59, 59, 59, 18, 18, 4, 1] 201
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: 938
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070981 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070981
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070981/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070981
Building REAL250005070982
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070982'
/scratch/stefan/7916153/working/building/REAL250005070982 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070982

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070982/0 /scratch/stefan/7916153/working/building/REAL250005070982 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 93)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/93
`/scratch/stefan/7916153/working/3D/93' -> `0.mol2'
Preparing input files

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

`REAL250005070982.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070982.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070982/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070982 none CC(C)[C@H](O)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 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', '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, 5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 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: [199, 180, 201, 123, 180, 180, 123, 123, 71, 25, 71, 67, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 540, 123, 71, 71, 71, 25, 25, 7, 1] 603
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: 1392
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070982 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070982
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070982/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070982
Building REAL250005070983
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070983'
/scratch/stefan/7916153/working/building/REAL250005070983 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070983

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070983/0 /scratch/stefan/7916153/working/building/REAL250005070983 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 94)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/94
`/scratch/stefan/7916153/working/3D/94' -> `0.mol2'
Preparing input files

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

`REAL250005070983.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070983.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070983/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070983 none C#CC1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 112, 112, 112, 75, 27, 75, 73, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 112, 75, 75, 75, 27, 27, 8, 1, 201, 201, 201, 201] 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: 699
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070983 none C#CC1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 7, 7, 7, 34, 34, 34, 117, 193, 193, 193, 201, 201, 201, 201, 201, 1, 1, 1, 7, 34, 34, 34, 117, 117, 193, 201, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 33, 32, 19, 20, 21, 30, 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])
total number of confs: 716
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070983 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070983
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070983/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070983
Building REAL250005070984
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070984'
/scratch/stefan/7916153/working/building/REAL250005070984 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070984

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070984/0 /scratch/stefan/7916153/working/building/REAL250005070984 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 95)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/95
`/scratch/stefan/7916153/working/3D/95' -> `0.mol2'
Preparing input files

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

`REAL250005070984.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070984.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070984/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070984 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCC(=O)O1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 5, 3, 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: [40, 11, 40, 40, 120, 169, 169, 169, 178, 178, 178, 178, 178, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 120, 120, 169, 178, 11, 1, 1, 1, 1] 178
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 648
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070984 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCC(=O)O1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 5, 3, 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: [77, 27, 79, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 79, 127, 127, 127, 178, 178, 178, 178, 178, 178, 79, 79, 79, 27, 27, 8, 1, 127, 178, 178, 178, 178] 178
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 644
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070984 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070984
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070984/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070984
Building REAL250005070985
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070985'
/scratch/stefan/7916153/working/building/REAL250005070985 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070985

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070985/0 /scratch/stefan/7916153/working/building/REAL250005070985 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 96)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/96
`/scratch/stefan/7916153/working/3D/96' -> `0.mol2'
Preparing input files

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

`REAL250005070985.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070985.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070985/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070985 none C=CC=CCC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', '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', '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, 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, 6, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 157, 67, 67, 67, 51, 17, 51, 51, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 157, 157, 67, 51, 51, 51, 17, 17, 4, 1] 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])
total number of confs: 810
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070985 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070985
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070985/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070985
Building REAL250005070986
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070986'
/scratch/stefan/7916153/working/building/REAL250005070986 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070986

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070986/0 /scratch/stefan/7916153/working/building/REAL250005070986 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 97)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/97
`/scratch/stefan/7916153/working/3D/97' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CCC1)

`REAL250005070986.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070986.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070986/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070986 none C#CC1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', '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', '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, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 6, 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, 4, 7, 6, 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, 102, 102, 102, 74, 27, 74, 72, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 102, 74, 74, 74, 27, 27, 8, 1, 201, 201, 201, 201, 201, 201] 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, 35, 36])
total number of confs: 688
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070986 none C#CC1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', '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', '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, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 32, 32, 32, 114, 196, 196, 196, 201, 201, 201, 201, 201, 1, 1, 1, 1, 7, 32, 32, 32, 114, 114, 196, 201, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 36, 33, 35, 32, 34, 19, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 714
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070986 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070986
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070986/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070986
Building REAL250005070987
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070987'
/scratch/stefan/7916153/working/building/REAL250005070987 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL250005070987

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070987/0 /scratch/stefan/7916153/working/building/REAL250005070987 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 98)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/98
`/scratch/stefan/7916153/working/3D/98' -> `0.mol2'
Preparing input files

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

`REAL250005070987.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070987.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070987/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070987 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC[N@@H+]1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [4, 2, 4, 4, 6, 6, 6, 6, 7, 7, 7, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 7, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2] 7
rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 31
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070987 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC[N@@H+]1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 7
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 19
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070987 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005070987/1 /scratch/stefan/7916153/working/building/REAL250005070987 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 99)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/99
`/scratch/stefan/7916153/working/3D/99' -> `1.mol2'
Preparing input files

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

`REAL250005070987.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005070987.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070987/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070987 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC[N@H+]1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [9, 5, 9, 9, 13, 13, 13, 13, 14, 14, 14, 14, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 13, 14, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2] 14
rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40])
total number of confs: 55
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070987 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCC[N@H+]1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 10, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12, 12, 10, 10, 8, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 14
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 43
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070987 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `2'
/scratch/stefan/7916153/working/building/REAL250005070987/2 /scratch/stefan/7916153/working/building/REAL250005070987 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 2 (index: 100)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/100
`/scratch/stefan/7916153/working/3D/100' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCCN1C)

`REAL250005070987.mol2' -> `2.mol2'
`temp.mol2' -> `REAL250005070987.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070987/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070987 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCCN1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 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: [19, 7, 19, 19, 55, 97, 97, 97, 105, 105, 105, 105, 105, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 55, 55, 97, 105, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2] 105
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39])
total number of confs: 361
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070987 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CCCN1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 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: [69, 29, 70, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 70, 101, 101, 101, 105, 105, 105, 105, 105, 105, 70, 70, 70, 28, 28, 8, 1, 101, 105, 105, 105, 105, 105, 105, 105, 105, 105] 105
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 398
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070987 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070987
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
2: /scratch/stefan/7916153/working/building/REAL250005070987/2.*
1: /scratch/stefan/7916153/working/building/REAL250005070987/1.*
0: /scratch/stefan/7916153/working/building/REAL250005070987/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070987
Building REAL250005070988
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070988'
/scratch/stefan/7916153/working/building/REAL250005070988 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070988

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070988/0 /scratch/stefan/7916153/working/building/REAL250005070988 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 101)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/101
`/scratch/stefan/7916153/working/3D/101' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC=CCO1)

`REAL250005070988.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070988.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070988/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070988 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC=CCO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [29, 9, 29, 29, 84, 135, 135, 135, 144, 144, 144, 144, 144, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 29, 84, 84, 135, 144, 9, 1, 1, 1, 1, 1, 1, 1] 144
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 522
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070988 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC=CCO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [77, 35, 79, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 79, 117, 117, 117, 144, 144, 144, 144, 144, 79, 79, 79, 35, 35, 10, 1, 117, 144, 144, 144, 144, 144, 144, 144] 144
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])
total number of confs: 530
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070988 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070988
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070988/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070988
Building REAL250005070989
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070989'
/scratch/stefan/7916153/working/building/REAL250005070989 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070989

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070989/0 /scratch/stefan/7916153/working/building/REAL250005070989 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 102)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/102
`/scratch/stefan/7916153/working/3D/102' -> `0.mol2'
Preparing input files

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

`REAL250005070989.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070989.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070989/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070989 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(C)(C)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [17, 6, 17, 17, 53, 84, 84, 84, 88, 88, 88, 88, 88, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 53, 53, 84, 88, 6, 1, 2, 2, 2, 2, 2, 2, 1, 1] 88
rigid atoms, others: [37, 38, 14, 16, 17, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36])
total number of confs: 328
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070989 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(C)(C)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [56, 26, 57, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 57, 88, 88, 88, 88, 88, 88, 88, 88, 57, 57, 57, 26, 26, 9, 1, 88, 88, 88, 88, 88, 88, 88, 88, 88, 88] 88
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: 332
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070989 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070989
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070989/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070989
Building REAL250005070990
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070990'
/scratch/stefan/7916153/working/building/REAL250005070990 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070990

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070990/0 /scratch/stefan/7916153/working/building/REAL250005070990 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 103)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/103
`/scratch/stefan/7916153/working/3D/103' -> `0.mol2'
Preparing input files

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

`REAL250005070990.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070990.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070990/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070990 none C#C[C@H]1C[C@H]1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 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', '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']
dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 154, 154, 119, 154, 119, 119, 78, 32, 78, 75, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 154, 154, 154, 119, 78, 78, 78, 31, 31, 8, 1] 154
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: 578
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070990 none C#C[C@H]1C[C@H]1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 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', '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']
dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 1, 1, 8, 8, 8, 36, 36, 36, 95, 146, 146, 146, 154, 154, 154, 154, 154, 1, 1, 1, 8, 36, 36, 36, 95, 95, 146, 154] 154
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])
total number of confs: 567
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070990 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070990
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070990/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070990
Building REAL250005070991
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070991'
/scratch/stefan/7916153/working/building/REAL250005070991 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070991

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070991/0 /scratch/stefan/7916153/working/building/REAL250005070991 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 104)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/104
`/scratch/stefan/7916153/working/3D/104' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(N=[N+]=[N-])CC1)

`REAL250005070991.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070991.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070991/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070991 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(N=[N+]=[N-])CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', '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, 8, 1, 11, 5, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 9, 26, 26, 73, 153, 153, 153, 163, 163, 163, 163, 163, 9, 1, 9, 1, 1, 13, 13, 1, 1, 26, 26, 26, 73, 73, 153, 163, 9, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 14, 16, 17, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 548
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070991 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(N=[N+]=[N-])CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', '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, 8, 1, 11, 5, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 19, 49, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 49, 81, 81, 81, 163, 201, 201, 163, 163, 49, 49, 49, 19, 19, 6, 1, 81, 163, 163, 163, 163] 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])
total number of confs: 601
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070991 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070991
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070991/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070991
Building REAL250005070992
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070992'
/scratch/stefan/7916153/working/building/REAL250005070992 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070992

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070992/0 /scratch/stefan/7916153/working/building/REAL250005070992 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 105)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/105
`/scratch/stefan/7916153/working/3D/105' -> `0.mol2'
Preparing input files

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

`REAL250005070992.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070992.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070992/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070992 none CCC(CC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)OC 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [172, 166, 123, 64, 64, 64, 37, 15, 37, 37, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 166, 168, 172, 172, 172, 172, 172, 166, 123, 123, 64, 37, 37, 37, 15, 15, 5, 1, 168, 168, 168] 172
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, 40])
total number of confs: 773
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070992 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070992
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070992/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070992
Building REAL250005070993
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070993'
/scratch/stefan/7916153/working/building/REAL250005070993 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070993

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070993/0 /scratch/stefan/7916153/working/building/REAL250005070993 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 106)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/106
`/scratch/stefan/7916153/working/3D/106' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSC=N1)

`REAL250005070993.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070993.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070993/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070993 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSC=N1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [15, 4, 15, 15, 46, 87, 87, 87, 93, 93, 93, 93, 93, 4, 1, 4, 1, 1, 1, 1, 1, 15, 15, 15, 46, 46, 87, 93, 4, 1, 1] 93
rigid atoms, others: [14, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 316
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070993 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSC=N1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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, 35, 69, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 92, 92, 92, 93, 93, 93, 93, 69, 69, 69, 35, 35, 9, 1, 92, 93, 93] 93
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])
total number of confs: 351
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070993 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070993
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070993/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070993
Building REAL250005070994
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070994'
/scratch/stefan/7916153/working/building/REAL250005070994 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070994

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070994/0 /scratch/stefan/7916153/working/building/REAL250005070994 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 107)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/107
`/scratch/stefan/7916153/working/3D/107' -> `0.mol2'
Preparing input files

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

`REAL250005070994.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070994.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070994/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070994 none CC=C(CC)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', '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', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [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: [164, 164, 75, 164, 201, 75, 75, 44, 14, 44, 44, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 201, 201, 201, 201, 201, 75, 44, 44, 44, 14, 14, 4, 1] 201
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: 758
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070994 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070994
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070994/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070994
Building REAL250005070995
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070995'
/scratch/stefan/7916153/working/building/REAL250005070995 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070995

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070995/0 /scratch/stefan/7916153/working/building/REAL250005070995 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 108)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/108
`/scratch/stefan/7916153/working/3D/108' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC12CC(C1)C2)

`REAL250005070995.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070995.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070995/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070995 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC12CC(C1)C2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 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: [72, 33, 72, 72, 131, 165, 165, 165, 177, 177, 177, 177, 177, 33, 9, 33, 1, 1, 1, 1, 1, 1, 72, 72, 72, 131, 131, 165, 177, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1] 177
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 686
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070995 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC12CC(C1)C2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 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: [79, 37, 79, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 79, 96, 96, 96, 177, 177, 177, 177, 177, 79, 79, 79, 37, 37, 11, 1, 96, 177, 177, 177, 177, 177, 177, 177, 177, 177] 177
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: 753
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070995 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070995
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070995/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070995
Building REAL250005070996
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070996'
/scratch/stefan/7916153/working/building/REAL250005070996 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070996

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070996/0 /scratch/stefan/7916153/working/building/REAL250005070996 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 109)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/109
`/scratch/stefan/7916153/working/3D/109' -> `0.mol2'
Preparing input files

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

`REAL250005070996.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070996.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070996/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070996 none CCC(C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)C(C)O 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', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6]
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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
279  conformations in input
total number of sets (complete confs): 279
using faster count positions algorithm for large data
unique positions, atoms: [84, 82, 49, 49, 49, 33, 14, 33, 33, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 82, 91, 93, 85, 85, 85, 85, 85, 82, 49, 33, 33, 33, 14, 14, 4, 1, 93, 93, 93, 93, 279] 279
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: 724
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070996 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070996
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070996/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070996
Building REAL250005070997
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070997'
/scratch/stefan/7916153/working/building/REAL250005070997 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070997

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070997/0 /scratch/stefan/7916153/working/building/REAL250005070997 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 110)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/110
`/scratch/stefan/7916153/working/3D/110' -> `0.mol2'
Preparing input files

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

`REAL250005070997.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070997.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070997/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005070997 none COC(F)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 15, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 113, 196, 113, 113, 69, 23, 69, 66, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 196, 113, 69, 69, 69, 23, 23, 7, 1] 201
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])
total number of confs: 844
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070997 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070997
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070997/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070997
Building REAL250005070998
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070998'
/scratch/stefan/7916153/working/building/REAL250005070998 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070998

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070998/0 /scratch/stefan/7916153/working/building/REAL250005070998 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 111)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/111
`/scratch/stefan/7916153/working/3D/111' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C#N)CCC1)

`REAL250005070998.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070998.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070998/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070998 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C#N)CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [25, 7, 25, 25, 73, 114, 114, 114, 117, 117, 117, 117, 117, 7, 1, 7, 1, 1, 1, 1, 1, 1, 25, 25, 25, 73, 73, 114, 117, 7, 1, 1, 1, 1, 1, 1] 117
rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 428
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070998 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C#N)CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [52, 19, 53, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 53, 79, 79, 79, 117, 117, 117, 117, 117, 53, 53, 53, 19, 19, 9, 1, 79, 117, 117, 117, 117, 117, 117] 117
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: 412
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070998 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070998
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070998/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070998
Building REAL250005070999
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005070999'
/scratch/stefan/7916153/working/building/REAL250005070999 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005070999

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005070999/0 /scratch/stefan/7916153/working/building/REAL250005070999 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 112)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/112
`/scratch/stefan/7916153/working/3D/112' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=C1CCCC1)

`REAL250005070999.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005070999.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005070999/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070999 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=C1CCCC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 45, 45, 141, 199, 199, 199, 201, 201, 201, 201, 201, 9, 1, 9, 1, 1, 1, 1, 1, 1, 45, 45, 45, 141, 141, 199, 201, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 746
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005070999 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=C1CCCC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 76, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 76, 116, 116, 116, 201, 201, 201, 201, 201, 76, 76, 76, 25, 25, 7, 1, 116, 201, 201, 201, 201, 201, 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, 38])
total number of confs: 697
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005070999 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005070999
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005070999/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005070999
Building REAL250005071000
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071000'
/scratch/stefan/7916153/working/building/REAL250005071000 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071000

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071000/0 /scratch/stefan/7916153/working/building/REAL250005071000 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 113)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/113
`/scratch/stefan/7916153/working/3D/113' -> `0.mol2'
Preparing input files

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

`REAL250005071000.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071000.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071000/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071000 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC(C)(C)C#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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [58, 27, 59, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 59, 89, 89, 89, 150, 184, 184, 184, 184, 59, 59, 59, 27, 27, 11, 1, 89, 150, 150, 184, 184, 184, 184, 184, 184] 184
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: 813
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071000 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071000
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071000/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071000
Building REAL250005071001
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071001'
/scratch/stefan/7916153/working/building/REAL250005071001 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071001

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071001/0 /scratch/stefan/7916153/working/building/REAL250005071001 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 114)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/114
`/scratch/stefan/7916153/working/3D/114' -> `0.mol2'
Preparing input files

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

`REAL250005071001.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071001.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071001/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071001 none COCC(O)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.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', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 3, 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]
1  hydrogens need rotated
591  conformations in input
total number of sets (complete confs): 591
using faster count positions algorithm for large data
unique positions, atoms: [197, 197, 155, 94, 155, 94, 94, 58, 23, 58, 58, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 155, 465, 94, 58, 58, 58, 23, 23, 8, 1] 591
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])
total number of confs: 1329
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071001 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071001
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071001/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071001
Building REAL250005071002
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071002'
/scratch/stefan/7916153/working/building/REAL250005071002 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071002

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071002/0 /scratch/stefan/7916153/working/building/REAL250005071002 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 115)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/115
`/scratch/stefan/7916153/working/3D/115' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC1(F)F)

`REAL250005071002.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071002.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071002/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071002 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC1(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [47, 13, 47, 47, 137, 185, 185, 185, 191, 191, 191, 191, 191, 13, 1, 13, 1, 1, 1, 1, 1, 1, 47, 47, 47, 137, 137, 185, 191, 13, 1, 1] 191
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 705
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071002 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC1(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [73, 28, 75, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 75, 113, 113, 113, 191, 191, 191, 191, 191, 75, 75, 75, 28, 28, 10, 1, 113, 191, 191] 191
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])
total number of confs: 657
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071002 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071002
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071002/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071002
Building REAL250005071003
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071003'
/scratch/stefan/7916153/working/building/REAL250005071003 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071003

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071003/0 /scratch/stefan/7916153/working/building/REAL250005071003 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 116)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/116
`/scratch/stefan/7916153/working/3D/116' -> `0.mol2'
Preparing input files

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

`REAL250005071003.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071003.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071003/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071003 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@H]1C#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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [44, 12, 44, 44, 141, 189, 189, 189, 201, 201, 201, 201, 201, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 141, 141, 189, 201, 12, 1, 1] 201
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 731
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071003 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@H]1C#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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [81, 33, 82, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 82, 113, 113, 113, 201, 201, 201, 201, 201, 201, 82, 82, 82, 32, 32, 9, 1, 113, 201, 201] 201
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32])
total number of confs: 708
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071003 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071003
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071003/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071003
Building REAL250005071004
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071004'
/scratch/stefan/7916153/working/building/REAL250005071004 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071004

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071004/0 /scratch/stefan/7916153/working/building/REAL250005071004 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 117)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/117
`/scratch/stefan/7916153/working/3D/117' -> `0.mol2'
Preparing input files

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

`REAL250005071004.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071004.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071004/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071004 none C=C(C)CCCC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 129, 121, 34, 34, 34, 25, 14, 25, 25, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 195, 192, 155, 155, 121, 121, 34, 25, 25, 25, 14, 14, 4, 1] 201
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: 1001
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071004 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071004
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071004/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071004
Building REAL250005071005
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071005'
/scratch/stefan/7916153/working/building/REAL250005071005 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071005

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071005/0 /scratch/stefan/7916153/working/building/REAL250005071005 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 118)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/118
`/scratch/stefan/7916153/working/3D/118' -> `0.mol2'
Preparing input files

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

`REAL250005071005.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071005.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071005/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071005 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1C[C@@H](O)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens 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, 12, 47, 47, 129, 191, 191, 191, 201, 201, 201, 201, 201, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 129, 129, 191, 201, 12, 1, 1, 3, 1, 1] 603
rigid atoms, others: [32, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 722
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071005 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1C[C@@H](O)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [71, 29, 72, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 72, 111, 111, 111, 201, 201, 201, 201, 201, 201, 72, 72, 72, 29, 29, 10, 1, 111, 201, 201, 603, 201, 201] 603
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35])
total number of confs: 1286
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071005 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071005
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071005/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071005
Building REAL250005071006
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071006'
/scratch/stefan/7916153/working/building/REAL250005071006 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071006

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071006/0 /scratch/stefan/7916153/working/building/REAL250005071006 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 119)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/119
`/scratch/stefan/7916153/working/3D/119' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC1(C)C)

`REAL250005071006.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071006.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071006/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071006 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC1(C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 40, 91, 91, 165, 201, 201, 201, 201, 201, 201, 201, 201, 40, 5, 40, 1, 1, 1, 1, 1, 1, 91, 91, 91, 165, 165, 201, 201, 40, 5, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201
rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40])
total number of confs: 832
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071006 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC1(C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 45, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 45, 67, 67, 67, 183, 201, 201, 201, 201, 45, 45, 45, 16, 16, 4, 1, 67, 183, 183, 201, 201, 201, 201, 201, 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, 38, 39, 40])
total number of confs: 793
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071006 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071006
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071006/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071006
Building REAL250005071007
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071007'
/scratch/stefan/7916153/working/building/REAL250005071007 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071007

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071007/0 /scratch/stefan/7916153/working/building/REAL250005071007 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 120)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/120
`/scratch/stefan/7916153/working/3D/120' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=C(Cl)CC1)

`REAL250005071007.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071007.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071007/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071007 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=C(Cl)CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [32, 12, 32, 32, 79, 120, 120, 120, 127, 127, 127, 127, 127, 12, 1, 12, 1, 1, 1, 1, 1, 32, 32, 32, 79, 79, 120, 127, 12, 1, 1, 1, 1] 127
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 448
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071007 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=C(Cl)CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [66, 27, 67, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 67, 106, 106, 106, 127, 127, 127, 127, 67, 67, 67, 27, 27, 9, 1, 106, 127, 127, 127, 127] 127
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])
total number of confs: 439
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071007 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071007
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071007/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071007
Building REAL250005071008
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071008'
/scratch/stefan/7916153/working/building/REAL250005071008 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071008

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071008/0 /scratch/stefan/7916153/working/building/REAL250005071008 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 121)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/121
`/scratch/stefan/7916153/working/3D/121' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](F)C2)

`REAL250005071008.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071008.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071008/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071008 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](F)C2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [34, 7, 34, 34, 117, 190, 190, 190, 199, 199, 199, 199, 199, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 117, 117, 190, 199, 7, 1, 1, 1, 1] 199
rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 701
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071008 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@]12C[C@H]1[C@H](F)C2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [76, 32, 77, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 77, 98, 98, 98, 199, 199, 199, 199, 199, 199, 199, 77, 77, 77, 31, 31, 9, 1, 98, 199, 199, 199, 199] 199
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35])
total number of confs: 523
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071008 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071008
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071008/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071008
Building REAL250005071009
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071009'
/scratch/stefan/7916153/working/building/REAL250005071009 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071009

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071009/0 /scratch/stefan/7916153/working/building/REAL250005071009 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 122)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/122
`/scratch/stefan/7916153/working/3D/122' -> `0.mol2'
Preparing input files

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

`REAL250005071009.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071009.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071009/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071009 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNC(=O)O1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [21, 8, 21, 21, 60, 100, 100, 100, 102, 102, 102, 102, 102, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 60, 60, 100, 102, 8, 1, 1] 102
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 363
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071009 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CNC(=O)O1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 11, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 6, 3, 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: [64, 26, 64, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 64, 97, 97, 97, 102, 102, 102, 102, 102, 64, 64, 64, 26, 26, 9, 1, 97, 102, 102] 102
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])
total number of confs: 370
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071009 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071009
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071009/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071009
Building REAL250005071010
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071010'
/scratch/stefan/7916153/working/building/REAL250005071010 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071010

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071010/0 /scratch/stefan/7916153/working/building/REAL250005071010 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 123)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/123
`/scratch/stefan/7916153/working/3D/123' -> `0.mol2'
Preparing input files

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

`REAL250005071010.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071010.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071010/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071010 none CC(C)[C@@H]1C[C@H]1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 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, 201, 201, 98, 201, 98, 98, 64, 21, 64, 62, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 98, 64, 64, 64, 20, 20, 7, 1] 201
rigid atoms, others: [40, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 659
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071010 none CC(C)[C@@H]1C[C@H]1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 47, 47, 47, 129, 199, 199, 199, 201, 201, 201, 201, 201, 4, 4, 4, 4, 4, 4, 4, 1, 1, 11, 47, 47, 47, 129, 129, 199, 201] 201
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 748
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071010 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071010
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071010/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071010
Building REAL250005071011
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071011'
/scratch/stefan/7916153/working/building/REAL250005071011 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071011

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071011/0 /scratch/stefan/7916153/working/building/REAL250005071011 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 124)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/124
`/scratch/stefan/7916153/working/3D/124' -> `0.mol2'
Preparing input files

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

`REAL250005071011.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071011.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071011/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071011 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COCCO 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', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [32, 10, 32, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 32, 46, 46, 46, 97, 165, 199, 201, 32, 32, 32, 10, 10, 4, 1, 46, 97, 97, 199, 199, 201, 201, 603] 603
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: 1316
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071011 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071011
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071011/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071011
Building REAL250005071012
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071012'
/scratch/stefan/7916153/working/building/REAL250005071012 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071012

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071012/0 /scratch/stefan/7916153/working/building/REAL250005071012 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 125)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/125
`/scratch/stefan/7916153/working/3D/125' -> `0.mol2'
Preparing input files

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

`REAL250005071012.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071012.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071012/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071012 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(C)CF 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 61, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 61, 107, 107, 107, 192, 192, 192, 201, 61, 61, 61, 20, 20, 6, 1, 107, 192, 192, 192, 192, 192, 192, 201, 201] 201
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, 36])
total number of confs: 834
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071012 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071012
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071012/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071012
Building REAL250005071013
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071013'
/scratch/stefan/7916153/working/building/REAL250005071013 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071013

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071013/0 /scratch/stefan/7916153/working/building/REAL250005071013 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 126)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/126
`/scratch/stefan/7916153/working/3D/126' -> `0.mol2'
Preparing input files

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

`REAL250005071013.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071013.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071013/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071013 none CC(C)[C@@H](O)CC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 4, 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]
1  hydrogens need rotated
582  conformations in input
total number of sets (complete confs): 582
using faster count positions algorithm for large data
unique positions, atoms: [194, 161, 194, 121, 161, 161, 70, 70, 70, 42, 17, 42, 42, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 194, 194, 194, 483, 121, 121, 70, 42, 42, 42, 17, 17, 5, 1] 582
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: 1415
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071013 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071013
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071013/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071013
Building REAL250005071014
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071014'
/scratch/stefan/7916153/working/building/REAL250005071014 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071014

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071014/0 /scratch/stefan/7916153/working/building/REAL250005071014 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 127)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/127
`/scratch/stefan/7916153/working/3D/127' -> `0.mol2'
Preparing input files

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

`REAL250005071014.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071014.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071014/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071014 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [63, 20, 65, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 65, 115, 115, 115, 190, 191, 190, 201, 65, 65, 65, 20, 20, 5, 1, 115, 190, 191, 191, 191, 191, 191, 200, 201, 603] 603
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, 36, 37])
total number of confs: 1451
number of broken/clashed sets: 90
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071014 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071014
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071014/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071014
Building REAL250005071015
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071015'
/scratch/stefan/7916153/working/building/REAL250005071015 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071015

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071015/0 /scratch/stefan/7916153/working/building/REAL250005071015 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 128)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/128
`/scratch/stefan/7916153/working/3D/128' -> `0.mol2'
Preparing input files

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

`REAL250005071015.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071015.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071015/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071015 none C=CCC(C)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', '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', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [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, 145, 70, 145, 70, 70, 47, 18, 47, 47, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 145, 145, 145, 145, 70, 47, 47, 47, 18, 18, 4, 1] 201
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: 909
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071015 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071015
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071015/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071015
Building REAL250005071016
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071016'
/scratch/stefan/7916153/working/building/REAL250005071016 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071016

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071016/0 /scratch/stefan/7916153/working/building/REAL250005071016 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 129)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/129
`/scratch/stefan/7916153/working/3D/129' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCC1C)

`REAL250005071016.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071016.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071016/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071016 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCC1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 40, 40, 126, 193, 193, 193, 201, 201, 201, 201, 201, 10, 1, 10, 1, 1, 1, 1, 1, 1, 40, 40, 40, 126, 126, 193, 201, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 30, 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, 38, 39, 40])
total number of confs: 722
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071016 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCC1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 73, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 73, 113, 113, 113, 201, 201, 201, 201, 201, 73, 73, 73, 28, 28, 8, 1, 113, 201, 201, 201, 201, 201, 201, 201, 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, 38, 39, 40])
total number of confs: 701
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071016 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071016
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071016/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071016
Building REAL250005071017
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071017'
/scratch/stefan/7916153/working/building/REAL250005071017 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071017

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071017/0 /scratch/stefan/7916153/working/building/REAL250005071017 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 130)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/130
`/scratch/stefan/7916153/working/3D/130' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC[C@@H]2C[C@@H]21)

`REAL250005071017.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071017.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071017/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071017 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC[C@@H]2C[C@@H]21 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 12, 54, 54, 147, 196, 196, 196, 201, 201, 201, 201, 201, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 147, 147, 196, 201, 12, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 750
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071017 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC[C@@H]2C[C@@H]21 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 72, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 72, 109, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 72, 72, 72, 25, 25, 9, 1, 109, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 697
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071017 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071017
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071017/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071017
Building REAL250005071018
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071018'
/scratch/stefan/7916153/working/building/REAL250005071018 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071018

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071018/0 /scratch/stefan/7916153/working/building/REAL250005071018 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 131)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/131
`/scratch/stefan/7916153/working/3D/131' -> `0.mol2'
Preparing input files

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

`REAL250005071018.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071018.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071018/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071018 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC(F)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [33, 6, 33, 33, 110, 178, 179, 178, 191, 191, 191, 191, 191, 6, 1, 6, 1, 1, 1, 1, 1, 1, 33, 33, 33, 110, 110, 179, 191, 6, 2, 2, 2, 1, 1, 1, 1, 1] 191
rigid atoms, others: [33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 684
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071018 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC(F)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [69, 27, 71, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 71, 101, 101, 101, 191, 191, 191, 191, 191, 71, 71, 71, 27, 27, 10, 1, 101, 191, 191, 191, 191, 191, 191, 191, 191] 191
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: 641
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071018 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071018
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071018/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071018
Building REAL250005071019
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071019'
/scratch/stefan/7916153/working/building/REAL250005071019 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071019

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071019/0 /scratch/stefan/7916153/working/building/REAL250005071019 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 132)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/132
`/scratch/stefan/7916153/working/3D/132' -> `0.mol2'
Preparing input files

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

`REAL250005071019.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071019.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071019/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071019 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@H]1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.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, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 47, 47, 128, 191, 191, 191, 201, 201, 201, 201, 201, 13, 1, 13, 1, 1, 1, 1, 1, 1, 47, 47, 47, 128, 128, 191, 201, 13, 1, 1, 2, 2, 2] 201
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 30, 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, 32, 33, 34])
total number of confs: 735
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071019 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1C[C@H]1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.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, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [76, 30, 77, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 77, 113, 113, 113, 201, 201, 201, 201, 201, 77, 77, 77, 30, 30, 9, 1, 113, 201, 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])
total number of confs: 704
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071019 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071019
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071019/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071019
Building REAL250005071020
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071020'
/scratch/stefan/7916153/working/building/REAL250005071020 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071020

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071020/0 /scratch/stefan/7916153/working/building/REAL250005071020 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 133)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/133
`/scratch/stefan/7916153/working/3D/133' -> `0.mol2'
Preparing input files

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

`REAL250005071020.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071020.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071020/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071020 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 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
423  conformations in input
total number of sets (complete confs): 423
using faster count positions algorithm for large data
unique positions, atoms: [88, 39, 88, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 88, 117, 117, 117, 141, 141, 141, 88, 88, 88, 39, 39, 10, 1, 117, 141, 141, 141, 141, 141, 141, 423] 423
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 990
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071020 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071020
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071020/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071020
Building REAL250005071021
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071021'
/scratch/stefan/7916153/working/building/REAL250005071021 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071021

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071021/0 /scratch/stefan/7916153/working/building/REAL250005071021 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 134)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/134
`/scratch/stefan/7916153/working/3D/134' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071021.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071021.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071021/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071021 none CSC1(C(=O)N[C@H](C)CNC(=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', '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', 'C.3', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 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, 178, 100, 100, 100, 60, 21, 60, 59, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 178, 178, 201, 201, 201, 100, 60, 60, 60, 21, 21, 6, 1, 178, 178, 178, 178] 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: 652
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071021 none CSC1(C(=O)N[C@H](C)CNC(=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', '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', 'C.3', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 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: [8, 1, 1, 1, 10, 10, 10, 38, 38, 38, 111, 172, 172, 172, 178, 178, 178, 178, 178, 1, 1, 8, 8, 8, 10, 38, 38, 38, 111, 111, 172, 178, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 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])
total number of confs: 648
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071021 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071021
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071021/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071021
Building REAL250005071022
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071022'
/scratch/stefan/7916153/working/building/REAL250005071022 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071022

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071022/0 /scratch/stefan/7916153/working/building/REAL250005071022 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 135)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/135
`/scratch/stefan/7916153/working/3D/135' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NOCC1)

`REAL250005071022.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071022.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071022/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071022 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NOCC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [31, 13, 31, 31, 80, 113, 113, 113, 118, 118, 118, 118, 118, 13, 1, 13, 1, 1, 1, 1, 1, 31, 31, 31, 80, 80, 113, 118, 13, 1, 1, 1, 1] 118
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 434
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071022 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NOCC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [69, 28, 70, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 70, 109, 109, 109, 118, 118, 118, 118, 70, 70, 70, 28, 28, 9, 1, 109, 118, 118, 118, 118] 118
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])
total number of confs: 427
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071022 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071022
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071022/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071022
Building REAL250005071023
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071023'
/scratch/stefan/7916153/working/building/REAL250005071023 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071023

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071023/0 /scratch/stefan/7916153/working/building/REAL250005071023 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 136)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/136
`/scratch/stefan/7916153/working/3D/136' -> `0.mol2'
Preparing input files

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

`REAL250005071023.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071023.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071023/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071023 none CC(C#N)CC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [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]
0  hydrogens 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, 186, 201, 201, 90, 90, 90, 54, 22, 54, 54, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 186, 186, 90, 54, 54, 54, 22, 22, 8, 1] 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])
total number of confs: 837
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071023 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071023
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071023/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071023
Building REAL250005071024
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071024'
/scratch/stefan/7916153/working/building/REAL250005071024 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL250005071024

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071024/0 /scratch/stefan/7916153/working/building/REAL250005071024 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 137)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/137
`/scratch/stefan/7916153/working/3D/137' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@H+](C)C1CC1)

`REAL250005071024.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071024.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071024/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071024 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@H+](C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [17, 12, 17, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 6, 12, 2, 1, 2, 2, 1, 1, 1, 17, 17, 17, 22, 22, 22, 22, 12, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1] 22
rigid atoms, others: [36, 37, 38, 39, 40, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 103
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071024 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@H+](C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [13, 9, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 15, 15, 15, 19, 22, 22, 22, 22, 22, 13, 13, 13, 9, 9, 4, 1, 15, 19, 19, 22, 22, 22, 22, 22, 22, 22, 22] 22
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 98
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071024 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071024/1 /scratch/stefan/7916153/working/building/REAL250005071024 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 138)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/138
`/scratch/stefan/7916153/working/3D/138' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@@H+](C)C1CC1)

`REAL250005071024.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071024.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071024/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071024 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@@H+](C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 9, 12, 12, 17, 18, 18, 18, 18, 18, 18, 18, 18, 9, 4, 9, 2, 1, 2, 2, 1, 1, 1, 12, 12, 12, 17, 17, 18, 18, 9, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1] 18
rigid atoms, others: [36, 37, 38, 39, 40, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 76
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071024 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@@H+](C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 9, 12, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 15, 15, 15, 17, 18, 18, 18, 18, 18, 12, 12, 12, 9, 9, 3, 1, 15, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18] 18
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 79
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071024 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `2'
/scratch/stefan/7916153/working/building/REAL250005071024/2 /scratch/stefan/7916153/working/building/REAL250005071024 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 2 (index: 139)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/139
`/scratch/stefan/7916153/working/3D/139' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN(C)C1CC1)

`REAL250005071024.mol2' -> `2.mol2'
`temp.mol2' -> `REAL250005071024.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071024/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071024 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN(C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 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: [29, 14, 29, 29, 58, 87, 87, 87, 87, 87, 87, 87, 87, 14, 8, 14, 3, 1, 3, 1, 1, 1, 29, 29, 29, 58, 58, 87, 87, 14, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1] 87
rigid atoms, others: [35, 36, 37, 38, 39, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 343
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071024 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN(C)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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 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: [43, 16, 45, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 45, 65, 65, 65, 86, 87, 87, 87, 87, 45, 45, 45, 16, 16, 4, 1, 65, 86, 86, 87, 87, 87, 87, 87, 87, 87, 87] 87
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, 39])
total number of confs: 369
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071024 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071024
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
2: /scratch/stefan/7916153/working/building/REAL250005071024/2.*
1: /scratch/stefan/7916153/working/building/REAL250005071024/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071024/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071024
Building REAL250005071025
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071025'
/scratch/stefan/7916153/working/building/REAL250005071025 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071025

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071025/0 /scratch/stefan/7916153/working/building/REAL250005071025 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 140)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/140
`/scratch/stefan/7916153/working/3D/140' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCOC1CC1)

`REAL250005071025.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071025.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071025/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071025 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCOC1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [132, 95, 132, 132, 174, 201, 201, 201, 201, 201, 201, 201, 201, 95, 44, 95, 26, 6, 1, 1, 1, 1, 132, 132, 132, 174, 174, 201, 201, 95, 44, 44, 26, 26, 1, 1, 1, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 851
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071025 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCOC1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 13, 31, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 31, 43, 43, 43, 109, 124, 169, 201, 201, 31, 31, 31, 13, 13, 4, 1, 43, 109, 109, 124, 124, 201, 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, 38])
total number of confs: 715
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071025 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071025
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071025/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071025
Building REAL250005071026
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071026'
/scratch/stefan/7916153/working/building/REAL250005071026 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071026

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071026/0 /scratch/stefan/7916153/working/building/REAL250005071026 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 141)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/141
`/scratch/stefan/7916153/working/3D/141' -> `0.mol2'
Preparing input files

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

`REAL250005071026.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071026.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071026/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071026 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCCCO 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [32, 14, 32, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 32, 38, 38, 38, 108, 134, 162, 178, 199, 32, 32, 32, 14, 14, 5, 1, 38, 108, 108, 155, 155, 161, 162, 201, 201, 198, 191, 597] 603
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, 39, 40])
total number of confs: 1750
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071026 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071026
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071026/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071026
Building REAL250005071027
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071027'
/scratch/stefan/7916153/working/building/REAL250005071027 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071027

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071027/0 /scratch/stefan/7916153/working/building/REAL250005071027 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 142)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/142
`/scratch/stefan/7916153/working/3D/142' -> `0.mol2'
Preparing input files

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

`REAL250005071027.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071027.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071027/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071027 none CC(CCO)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 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
435  conformations in input
total number of sets (complete confs): 435
using faster count positions algorithm for large data
unique positions, atoms: [119, 51, 119, 143, 145, 51, 51, 43, 18, 43, 43, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 143, 143, 145, 145, 435, 51, 43, 43, 43, 18, 18, 4, 1] 435
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: 1076
number of broken/clashed sets: 85
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071027 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071027
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071027/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071027
Building REAL250005071028
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071028'
/scratch/stefan/7916153/working/building/REAL250005071028 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071028

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071028/0 /scratch/stefan/7916153/working/building/REAL250005071028 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 143)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/143
`/scratch/stefan/7916153/working/3D/143' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)=CC1CC1)

`REAL250005071028.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071028.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071028/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071028 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)=CC1CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 81, 81, 153, 201, 201, 201, 201, 201, 201, 201, 201, 37, 7, 37, 7, 7, 1, 1, 1, 1, 81, 81, 81, 153, 153, 201, 201, 37, 7, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 767
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071028 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(F)=CC1CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 21, 67, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 67, 123, 123, 123, 152, 153, 153, 201, 201, 67, 67, 67, 21, 21, 4, 1, 123, 153, 201, 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])
total number of confs: 731
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071028 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071028
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071028/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071028
Building REAL250005071029
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071029'
/scratch/stefan/7916153/working/building/REAL250005071029 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071029

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071029/0 /scratch/stefan/7916153/working/building/REAL250005071029 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 144)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/144
`/scratch/stefan/7916153/working/3D/144' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(F)C1)

`REAL250005071029.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071029.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071029/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071029 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(F)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [90, 38, 90, 90, 159, 201, 201, 201, 201, 201, 201, 201, 201, 38, 7, 38, 1, 1, 1, 1, 1, 1, 90, 90, 90, 159, 159, 201, 201, 38, 7, 7, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 802
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071029 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(F)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [46, 17, 46, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 46, 73, 73, 73, 175, 201, 201, 201, 201, 46, 46, 46, 17, 17, 4, 1, 73, 175, 175, 201, 201, 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: 792
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071029 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071029
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071029/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071029
Building REAL250005071030
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071030'
/scratch/stefan/7916153/working/building/REAL250005071030 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071030

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071030/0 /scratch/stefan/7916153/working/building/REAL250005071030 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 145)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/145
`/scratch/stefan/7916153/working/3D/145' -> `0.mol2'
Preparing input files

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

`REAL250005071030.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071030.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071030/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071030 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](O)CF 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 12, 5, 15, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [72, 27, 74, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 74, 121, 121, 121, 183, 183, 183, 201, 74, 74, 74, 27, 27, 9, 1, 121, 549, 201, 201] 603
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])
total number of confs: 1387
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071030 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071030
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071030/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071030
Building REAL250005071031
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071031'
/scratch/stefan/7916153/working/building/REAL250005071031 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071031

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071031/0 /scratch/stefan/7916153/working/building/REAL250005071031 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 146)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/146
`/scratch/stefan/7916153/working/3D/146' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CCO)CC1)

`REAL250005071031.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071031.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071031/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071031 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CCO)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
387  conformations in input
total number of sets (complete confs): 387
using faster count positions algorithm for large data
unique positions, atoms: [20, 7, 20, 20, 54, 99, 99, 99, 105, 105, 105, 105, 105, 7, 1, 7, 1, 1, 7, 12, 1, 1, 20, 20, 20, 54, 54, 99, 105, 7, 7, 7, 12, 12, 36, 1, 1, 1, 1] 387
rigid atoms, others: [35, 36, 37, 38, 14, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 441
number of broken/clashed sets: 49
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071031 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(CCO)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
387  conformations in input
total number of sets (complete confs): 387
using faster count positions algorithm for large data
unique positions, atoms: [34, 15, 34, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 34, 63, 63, 63, 105, 129, 129, 105, 105, 34, 34, 34, 15, 15, 5, 1, 63, 129, 129, 129, 129, 387, 105, 105, 105, 105] 387
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: 894
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071031 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071031
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071031/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071031
Building REAL250005071032
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071032'
/scratch/stefan/7916153/working/building/REAL250005071032 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071032

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071032/0 /scratch/stefan/7916153/working/building/REAL250005071032 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 147)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/147
`/scratch/stefan/7916153/working/3D/147' -> `0.mol2'
Preparing input files

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

`REAL250005071032.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071032.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071032/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071032 none CC(C)C(C)(O)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 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: [197, 196, 201, 134, 196, 196, 134, 134, 78, 26, 78, 76, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 196, 196, 196, 588, 134, 78, 78, 78, 26, 26, 7, 1] 603
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: 1446
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071032 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071032
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071032/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071032
Building REAL250005071033
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071033'
/scratch/stefan/7916153/working/building/REAL250005071033 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071033

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071033/0 /scratch/stefan/7916153/working/building/REAL250005071033 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 148)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/148
`/scratch/stefan/7916153/working/3D/148' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CCC1)

`REAL250005071033.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071033.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071033/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071033 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 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
387  conformations in input
total number of sets (complete confs): 387
using faster count positions algorithm for large data
unique positions, atoms: [36, 10, 36, 36, 85, 123, 123, 123, 129, 129, 129, 129, 129, 10, 1, 10, 1, 1, 1, 1, 1, 36, 36, 36, 85, 85, 123, 129, 10, 6, 1, 1, 1, 1, 1, 1] 387
rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 485
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071033 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 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
387  conformations in input
total number of sets (complete confs): 387
using faster count positions algorithm for large data
unique positions, atoms: [63, 22, 65, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 65, 90, 90, 90, 129, 129, 129, 129, 65, 65, 65, 22, 22, 9, 1, 90, 387, 129, 129, 129, 129, 129, 129] 387
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: 853
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071033 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071033
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071033/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071033
Building REAL250005071034
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071034'
/scratch/stefan/7916153/working/building/REAL250005071034 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071034

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071034/0 /scratch/stefan/7916153/working/building/REAL250005071034 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 149)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/149
`/scratch/stefan/7916153/working/3D/149' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(O)C1CC1)

`REAL250005071034.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071034.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071034/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071034 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 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
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [76, 33, 76, 76, 152, 198, 198, 198, 201, 201, 201, 201, 201, 33, 8, 33, 1, 8, 1, 1, 1, 76, 76, 76, 152, 152, 198, 201, 33, 8, 24, 1, 1, 1, 1, 1] 603
rigid atoms, others: [32, 33, 34, 35, 16, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 814
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071034 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 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
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [70, 25, 72, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 72, 111, 111, 111, 156, 156, 201, 201, 72, 72, 72, 25, 25, 8, 1, 111, 156, 468, 201, 201, 201, 201, 201] 603
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: 1284
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071034 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071034
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071034/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071034
Building REAL250005071035
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071035'
/scratch/stefan/7916153/working/building/REAL250005071035 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071035

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071035/0 /scratch/stefan/7916153/working/building/REAL250005071035 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 150)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/150
`/scratch/stefan/7916153/working/3D/150' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NN=C1)

`REAL250005071035.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071035.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071035/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071035 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NN=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [59, 31, 59, 59, 86, 104, 104, 104, 115, 115, 115, 115, 115, 31, 7, 31, 1, 1, 1, 1, 1, 1, 59, 59, 59, 86, 86, 104, 115, 31, 7, 7, 1, 1] 115
rigid atoms, others: [32, 33, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 439
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071035 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NN=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [42, 23, 42, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 42, 66, 66, 66, 114, 117, 117, 117, 117, 42, 42, 42, 23, 23, 10, 1, 66, 114, 114, 117, 117] 117
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])
total number of confs: 483
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071035 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071035
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071035/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071035
Building REAL250005071036
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071036'
/scratch/stefan/7916153/working/building/REAL250005071036 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071036

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071036/0 /scratch/stefan/7916153/working/building/REAL250005071036 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 151)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/151
`/scratch/stefan/7916153/working/3D/151' -> `0.mol2'
Preparing input files

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

`REAL250005071036.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071036.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071036/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071036 none C=C(C)CC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 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', '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: [1, 1, 5, 5, 1, 11, 8, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 199, 201, 115, 115, 115, 82, 31, 82, 82, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 199, 199, 115, 82, 82, 82, 31, 31, 9, 1] 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])
total number of confs: 844
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071036 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071036
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071036/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071036
Building REAL250005071037
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071037'
/scratch/stefan/7916153/working/building/REAL250005071037 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071037

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071037/0 /scratch/stefan/7916153/working/building/REAL250005071037 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 152)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/152
`/scratch/stefan/7916153/working/3D/152' -> `0.mol2'
Preparing input files

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

`REAL250005071037.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071037.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071037/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071037 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(C)(C)C#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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', '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, 8, 1, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [49, 19, 51, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 51, 70, 70, 70, 100, 100, 100, 100, 51, 51, 51, 19, 19, 8, 1, 70, 100, 100, 100, 100, 100, 100] 100
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])
total number of confs: 398
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071037 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071037
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071037/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071037
Building REAL250005071038
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071038'
/scratch/stefan/7916153/working/building/REAL250005071038 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071038

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071038/0 /scratch/stefan/7916153/working/building/REAL250005071038 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 153)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/153
`/scratch/stefan/7916153/working/3D/153' -> `0.mol2'
Preparing input files

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

`REAL250005071038.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071038.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071038/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071038 none CCSCC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.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', '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, 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, 6, 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]
0  hydrogens need 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, 123, 70, 70, 70, 41, 15, 41, 41, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 123, 123, 70, 41, 41, 41, 15, 15, 4, 1] 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])
total number of confs: 826
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071038 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071038
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071038/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071038
Building REAL250005071039
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071039'
/scratch/stefan/7916153/working/building/REAL250005071039 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071039

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071039/0 /scratch/stefan/7916153/working/building/REAL250005071039 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 154)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/154
`/scratch/stefan/7916153/working/3D/154' -> `0.mol2'
Preparing input files

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

`REAL250005071039.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071039.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071039/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071039 none CC(=O)OCCC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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']
dock atom type numbers: [5, 1, 11, 12, 5, 5, 1, 11, 8, 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, 6, 7]
dock color type numbers: [7, 7, 5, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 154, 140, 60, 60, 60, 45, 18, 45, 45, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 154, 154, 140, 140, 60, 45, 45, 45, 18, 18, 4, 1] 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])
total number of confs: 730
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071039 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071039
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071039/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071039
Building REAL250005071040
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071040'
/scratch/stefan/7916153/working/building/REAL250005071040 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071040

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071040/0 /scratch/stefan/7916153/working/building/REAL250005071040 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 155)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/155
`/scratch/stefan/7916153/working/3D/155' -> `0.mol2'
Preparing input files

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

`REAL250005071040.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071040.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071040/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071040 none CC(C)=C(C)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', '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', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [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
147  conformations in input
total number of sets (complete confs): 147
using faster count positions algorithm for large data
unique positions, atoms: [147, 147, 147, 115, 147, 115, 115, 79, 33, 79, 77, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 147, 147, 147, 147, 147, 115, 79, 79, 79, 33, 33, 10, 1] 147
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: 560
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071040 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071040
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071040/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071040
Building REAL250005071041
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071041'
/scratch/stefan/7916153/working/building/REAL250005071041 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071041

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071041/0 /scratch/stefan/7916153/working/building/REAL250005071041 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 156)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/156
`/scratch/stefan/7916153/working/3D/156' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC1(C)N=N1)

`REAL250005071041.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071041.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071041/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071041 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC1(C)N=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 58, 98, 98, 166, 201, 201, 201, 201, 201, 201, 201, 201, 58, 12, 58, 8, 1, 1, 1, 1, 1, 98, 98, 98, 166, 166, 201, 201, 58, 12, 12, 8, 8, 2, 2, 2] 201
rigid atoms, others: [17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 824
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071041 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCC1(C)N=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 13, 29, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 29, 43, 43, 43, 137, 154, 201, 201, 201, 29, 29, 29, 13, 13, 4, 1, 43, 137, 137, 163, 163, 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])
total number of confs: 847
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071041 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071041
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071041/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071041
Building REAL250005071042
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071042'
/scratch/stefan/7916153/working/building/REAL250005071042 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071042

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071042/0 /scratch/stefan/7916153/working/building/REAL250005071042 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 157)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/157
`/scratch/stefan/7916153/working/3D/157' -> `0.mol2'
Preparing input files

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

`REAL250005071042.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071042.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071042/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071042 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=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', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [9, 2, 9, 9, 18, 25, 25, 25, 31, 31, 31, 31, 31, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 18, 18, 25, 31, 2, 1] 31
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 104
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071042 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=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', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [24, 18, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 24, 31, 31, 31, 31, 31, 31, 31, 31, 24, 24, 24, 18, 18, 7, 1, 31, 31] 31
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])
total number of confs: 113
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071042 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071042
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071042/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071042
Building REAL250005071043
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071043'
/scratch/stefan/7916153/working/building/REAL250005071043 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071043

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071043/0 /scratch/stefan/7916153/working/building/REAL250005071043 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 158)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/158
`/scratch/stefan/7916153/working/3D/158' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COC1COC1)

`REAL250005071043.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071043.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071043/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071043 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COC1COC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [114, 74, 114, 114, 157, 201, 201, 201, 201, 201, 201, 201, 201, 74, 25, 74, 6, 1, 1, 1, 1, 1, 114, 114, 114, 157, 157, 201, 201, 74, 25, 25, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 790
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071043 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)COC1COC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 10, 32, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 32, 49, 49, 49, 123, 168, 201, 201, 201, 32, 32, 32, 10, 10, 4, 1, 49, 123, 123, 201, 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])
total number of confs: 709
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071043 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071043
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071043/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071043
Building REAL250005071044
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071044'
/scratch/stefan/7916153/working/building/REAL250005071044 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071044

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071044/0 /scratch/stefan/7916153/working/building/REAL250005071044 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 159)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/159
`/scratch/stefan/7916153/working/3D/159' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@]12C[C@@H]1[C@H](C)C2)

`REAL250005071044.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071044.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071044/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071044 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@]12C[C@@H]1[C@H](C)C2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 7, 34, 34, 113, 190, 190, 190, 201, 201, 201, 201, 201, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 113, 113, 190, 201, 7, 1, 1, 2, 2, 2, 1, 1] 201
rigid atoms, others: [32, 33, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36])
total number of confs: 708
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071044 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@]12C[C@@H]1[C@H](C)C2 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 7, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 77, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 77, 100, 100, 100, 201, 201, 201, 201, 201, 201, 201, 77, 77, 77, 31, 31, 10, 1, 100, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 536
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071044 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071044
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071044/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071044
Building REAL250005071045
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071045'
/scratch/stefan/7916153/working/building/REAL250005071045 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071045

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071045/0 /scratch/stefan/7916153/working/building/REAL250005071045 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 160)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/160
`/scratch/stefan/7916153/working/3D/160' -> `0.mol2'
Preparing input files

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

`REAL250005071045.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071045.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071045/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071045 none CNC(=O)CC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.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', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 4, 7, 6, 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
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [81, 81, 72, 81, 54, 54, 54, 39, 19, 39, 39, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 72, 72, 54, 39, 39, 39, 19, 19, 8, 1] 81
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: 339
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071045 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071045
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071045/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071045
Building REAL250005071046
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071046'
/scratch/stefan/7916153/working/building/REAL250005071046 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071046

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071046/0 /scratch/stefan/7916153/working/building/REAL250005071046 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 161)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/161
`/scratch/stefan/7916153/working/3D/161' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN=CN1C)

`REAL250005071046.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071046.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071046/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071046 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN=CN1C 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', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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, 8, 1, 11, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [15, 4, 15, 15, 55, 97, 97, 97, 98, 98, 98, 98, 98, 4, 1, 4, 1, 1, 1, 1, 1, 1, 15, 15, 15, 55, 55, 97, 98, 4, 1, 2, 2, 2] 98
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33])
total number of confs: 355
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071046 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=NN=CN1C 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', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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, 8, 1, 11, 1, 8, 8, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [68, 25, 69, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 98, 98, 98, 98, 98, 98, 98, 98, 69, 69, 69, 25, 25, 9, 1, 98, 98, 98, 98, 98] 98
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])
total number of confs: 355
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071046 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071046
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071046/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071046
Building REAL250005071047
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071047'
/scratch/stefan/7916153/working/building/REAL250005071047 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071047

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071047/0 /scratch/stefan/7916153/working/building/REAL250005071047 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 162)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/162
`/scratch/stefan/7916153/working/3D/162' -> `0.mol2'
Preparing input files

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

`REAL250005071047.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071047.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071047/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071047 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCO[C@H]1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [20, 5, 20, 20, 72, 114, 114, 114, 121, 121, 121, 121, 121, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 72, 72, 114, 121, 5, 1, 1, 1, 1, 2, 2, 2] 121
rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38])
total number of confs: 438
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071047 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CCO[C@H]1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [67, 25, 69, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 104, 104, 104, 121, 121, 121, 121, 121, 121, 121, 69, 69, 69, 25, 25, 9, 1, 104, 121, 121, 121, 121, 121, 121, 121] 121
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 463
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071047 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071047
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071047/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071047
Building REAL250005071048
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071048'
/scratch/stefan/7916153/working/building/REAL250005071048 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071048

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071048/0 /scratch/stefan/7916153/working/building/REAL250005071048 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 163)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/163
`/scratch/stefan/7916153/working/3D/163' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(F)C1)

`REAL250005071048.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071048.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071048/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071048 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(F)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 46, 46, 129, 192, 192, 192, 201, 201, 201, 201, 201, 11, 1, 11, 1, 1, 1, 1, 1, 46, 46, 46, 129, 129, 192, 201, 11, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 719
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071048 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(F)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 75, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 75, 113, 113, 113, 201, 201, 201, 201, 75, 75, 75, 30, 30, 10, 1, 113, 201, 201, 201, 201, 201, 201] 201
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])
total number of confs: 706
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071048 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071048
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071048/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071048
Building REAL250005071049
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071049'
/scratch/stefan/7916153/working/building/REAL250005071049 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071049

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071049/0 /scratch/stefan/7916153/working/building/REAL250005071049 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 164)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/164
`/scratch/stefan/7916153/working/3D/164' -> `0.mol2'
Preparing input files

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

`REAL250005071049.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071049.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071049/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071049 none CCC(O)C(C)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 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]
1  hydrogens need rotated
375  conformations in input
total number of sets (complete confs): 375
using faster count positions algorithm for large data
unique positions, atoms: [125, 118, 95, 119, 62, 95, 62, 62, 36, 16, 36, 36, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 125, 119, 357, 95, 95, 95, 95, 62, 36, 36, 36, 16, 16, 5, 1] 375
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: 936
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071049 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071049
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071049/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071049
Building REAL250005071050
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071050'
/scratch/stefan/7916153/working/building/REAL250005071050 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071050

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071050/0 /scratch/stefan/7916153/working/building/REAL250005071050 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 165)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/165
`/scratch/stefan/7916153/working/3D/165' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(=O)N1)

`REAL250005071050.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071050.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071050/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071050 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [89, 43, 89, 89, 162, 200, 200, 200, 201, 201, 201, 201, 201, 43, 7, 43, 1, 1, 1, 1, 1, 1, 89, 89, 89, 162, 162, 200, 201, 43, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 795
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071050 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 20, 53, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 53, 87, 87, 87, 177, 201, 201, 201, 201, 53, 53, 53, 20, 20, 6, 1, 87, 177, 177, 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])
total number of confs: 790
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071050 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071050
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071050/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071050
Building REAL250005071051
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071051'
/scratch/stefan/7916153/working/building/REAL250005071051 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071051

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071051/0 /scratch/stefan/7916153/working/building/REAL250005071051 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 166)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/166
`/scratch/stefan/7916153/working/3D/166' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(O)C1CCC1)

`REAL250005071051.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071051.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071051/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071051 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(O)C1CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [75, 35, 75, 75, 153, 197, 197, 197, 201, 201, 201, 201, 201, 35, 6, 35, 1, 6, 1, 1, 1, 1, 75, 75, 75, 153, 153, 197, 201, 35, 6, 18, 1, 1, 1, 1, 1, 1, 1] 603
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 16, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 786
number of broken/clashed sets: 70
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071051 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(O)C1CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [62, 21, 63, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 63, 110, 110, 110, 162, 162, 201, 201, 201, 63, 63, 63, 21, 21, 7, 1, 110, 162, 486, 201, 201, 201, 201, 201, 201, 201] 603
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: 1277
number of broken/clashed sets: 70
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071051 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071051
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071051/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071051
Building REAL250005071052
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071052'
/scratch/stefan/7916153/working/building/REAL250005071052 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071052

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071052/0 /scratch/stefan/7916153/working/building/REAL250005071052 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 167)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/167
`/scratch/stefan/7916153/working/3D/167' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1C[NH+](C)C1)

`REAL250005071052.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071052.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071052/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071052 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1C[NH+](C)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [13, 8, 13, 13, 16, 16, 16, 16, 18, 18, 18, 18, 18, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 16, 16, 16, 18, 8, 5, 5, 1, 1, 1, 2, 2, 2, 1, 1] 18
rigid atoms, others: [33, 34, 35, 39, 40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38])
total number of confs: 78
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071052 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1C[NH+](C)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [14, 11, 14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 15, 15, 15, 18, 18, 18, 18, 18, 18, 14, 14, 14, 11, 11, 7, 1, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 18
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 73
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071052 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071052
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071052/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071052
Building REAL250005071053
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071053'
/scratch/stefan/7916153/working/building/REAL250005071053 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071053

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071053/0 /scratch/stefan/7916153/working/building/REAL250005071053 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 168)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/168
`/scratch/stefan/7916153/working/3D/168' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(O)C1)

`REAL250005071053.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071053.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071053/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071053 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(O)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [47, 11, 47, 47, 138, 196, 196, 196, 201, 201, 201, 201, 201, 11, 1, 11, 1, 1, 1, 1, 1, 1, 47, 47, 47, 138, 138, 196, 201, 11, 1, 1, 1, 2, 2, 2, 6, 1, 1] 603
rigid atoms, others: [32, 37, 38, 14, 16, 17, 18, 19, 20, 21, 30, 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, 33, 34, 35, 36])
total number of confs: 741
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071053 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(C)(O)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [78, 28, 80, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 80, 126, 126, 126, 201, 201, 201, 201, 201, 80, 80, 80, 28, 28, 9, 1, 126, 201, 201, 201, 201, 201, 201, 603, 201, 201] 603
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: 1323
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071053 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071053
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071053/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071053
Building REAL250005071054
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071054'
/scratch/stefan/7916153/working/building/REAL250005071054 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071054

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071054/0 /scratch/stefan/7916153/working/building/REAL250005071054 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 169)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/169
`/scratch/stefan/7916153/working/3D/169' -> `0.mol2'
Preparing input files

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

`REAL250005071054.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071054.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071054/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071054 none C=CCC(=O)N[C@H](C)CNC(=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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 124, 124, 91, 36, 91, 91, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 200, 124, 91, 91, 91, 36, 36, 10, 1] 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])
total number of confs: 858
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071054 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071054
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071054/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071054
Building REAL250005071055
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071055'
/scratch/stefan/7916153/working/building/REAL250005071055 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071055

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071055/0 /scratch/stefan/7916153/working/building/REAL250005071055 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 170)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/170
`/scratch/stefan/7916153/working/3D/170' -> `0.mol2'
Preparing input files

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

`REAL250005071055.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071055.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071055/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071055 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[NH+](C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [13, 9, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 14, 14, 14, 14, 13, 13, 13, 9, 9, 6, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14] 14
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, 36])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071055 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071055/1 /scratch/stefan/7916153/working/building/REAL250005071055 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 171)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/171
`/scratch/stefan/7916153/working/3D/171' -> `1.mol2'
Preparing input files

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

`REAL250005071055.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071055.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071055/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.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: REAL250005071055 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN(C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', '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, 8, 1, 11, 5, 10, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
193  conformations in input
total number of sets (complete confs): 193
using faster count positions algorithm for large data
unique positions, atoms: [95, 41, 97, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 97, 142, 142, 142, 193, 193, 193, 97, 97, 97, 41, 41, 10, 1, 142, 193, 193, 193, 193, 193, 193, 193, 193] 193
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 812
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071055 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071055
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071055/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071055/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071055
Building REAL250005071056
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071056'
/scratch/stefan/7916153/working/building/REAL250005071056 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071056

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071056/0 /scratch/stefan/7916153/working/building/REAL250005071056 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 172)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/172
`/scratch/stefan/7916153/working/3D/172' -> `0.mol2'
Preparing input files

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

`REAL250005071056.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071056.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071056/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071056 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', '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, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [53, 24, 53, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 53, 74, 74, 74, 109, 109, 53, 53, 53, 24, 24, 9, 1, 74, 109, 109] 109
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 25] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28])
total number of confs: 451
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071056 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071056
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071056/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071056
Building REAL250005071057
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071057'
/scratch/stefan/7916153/working/building/REAL250005071057 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071057

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071057/0 /scratch/stefan/7916153/working/building/REAL250005071057 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 173)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/173
`/scratch/stefan/7916153/working/3D/173' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC1F)

`REAL250005071057.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071057.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071057/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071057 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC1F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [43, 12, 43, 43, 117, 175, 175, 175, 187, 187, 187, 187, 187, 12, 1, 12, 1, 1, 1, 1, 43, 43, 43, 117, 117, 175, 187, 12, 1, 1, 1, 1] 187
rigid atoms, others: [14, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 679
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071057 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC1F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [78, 30, 79, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 79, 114, 114, 114, 187, 187, 187, 79, 79, 79, 30, 30, 9, 1, 114, 187, 187, 187, 187] 187
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31])
total number of confs: 670
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071057 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071057
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071057/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071057
Building REAL250005071058
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071058'
/scratch/stefan/7916153/working/building/REAL250005071058 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071058

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071058/0 /scratch/stefan/7916153/working/building/REAL250005071058 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 174)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/174
`/scratch/stefan/7916153/working/3D/174' -> `0.mol2'
Preparing input files

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

`REAL250005071058.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071058.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071058/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071058 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](C)[NH+](C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [14, 13, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 16, 16, 16, 17, 17, 17, 14, 14, 14, 13, 13, 8, 1, 14, 16, 16, 16, 17, 17, 17, 17, 17, 17] 17
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 68
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071058 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071058/1 /scratch/stefan/7916153/working/building/REAL250005071058 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 175)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/175
`/scratch/stefan/7916153/working/3D/175' -> `1.mol2'
Preparing input files

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

`REAL250005071058.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071058.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071058/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.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: REAL250005071058 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H](C)N(C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 10, 5, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 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: [65, 29, 66, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 66, 88, 88, 88, 116, 116, 116, 117, 117, 66, 66, 66, 29, 29, 9, 1, 88, 116, 116, 116, 117, 117, 117, 117, 117, 117] 117
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: 474
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071058 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071058
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071058/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071058/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071058
Building REAL250005071059
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071059'
/scratch/stefan/7916153/working/building/REAL250005071059 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071059

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071059/0 /scratch/stefan/7916153/working/building/REAL250005071059 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 176)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/176
`/scratch/stefan/7916153/working/3D/176' -> `0.mol2'
Preparing input files

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

`REAL250005071059.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071059.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071059/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071059 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', '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, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 25, 70, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 70, 106, 106, 106, 198, 201, 70, 70, 70, 25, 25, 8, 1, 106, 198, 198, 201, 201] 201
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 25] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30])
total number of confs: 798
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071059 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071059
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071059/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071059
Building REAL250005071060
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071060'
/scratch/stefan/7916153/working/building/REAL250005071060 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071060

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071060/0 /scratch/stefan/7916153/working/building/REAL250005071060 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 177)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/177
`/scratch/stefan/7916153/working/3D/177' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(F)=NN1)

`REAL250005071060.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071060.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071060/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071060 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(F)=NN1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 15, 8, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 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: [17, 7, 17, 17, 46, 75, 75, 75, 80, 80, 80, 80, 80, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 46, 46, 75, 80, 7, 1, 1] 80
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 281
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071060 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CC(F)=NN1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 1, 15, 8, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 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: [46, 21, 46, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 46, 72, 72, 72, 80, 80, 80, 80, 80, 46, 46, 46, 21, 21, 9, 1, 72, 80, 80] 80
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])
total number of confs: 278
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071060 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071060
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071060/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071060
Building REAL250005071061
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071061'
/scratch/stefan/7916153/working/building/REAL250005071061 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071061

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071061/0 /scratch/stefan/7916153/working/building/REAL250005071061 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 178)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/178
`/scratch/stefan/7916153/working/3D/178' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1C=CCC1)

`REAL250005071061.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071061.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071061/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071061 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1C=CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 12, 42, 42, 128, 191, 191, 191, 201, 201, 201, 201, 201, 12, 1, 12, 1, 1, 1, 1, 1, 42, 42, 42, 128, 128, 191, 201, 12, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 729
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071061 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1C=CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 83, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 83, 119, 119, 119, 201, 201, 201, 201, 83, 83, 83, 31, 31, 10, 1, 119, 201, 201, 201, 201, 201, 201, 201] 201
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: 701
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071061 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071061
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071061/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071061
Building REAL250005071062
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071062'
/scratch/stefan/7916153/working/building/REAL250005071062 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071062

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071062/0 /scratch/stefan/7916153/working/building/REAL250005071062 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 179)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/179
`/scratch/stefan/7916153/working/3D/179' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)COC1)

`REAL250005071062.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071062.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071062/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071062 none CCC1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)COC1 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', '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, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [167, 164, 97, 97, 97, 59, 22, 59, 57, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 164, 164, 164, 167, 167, 167, 167, 167, 97, 59, 59, 59, 22, 22, 9, 1, 164, 164, 164, 164] 167
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: 583
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071062 none CCC1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)COC1 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', '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, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 6, 6, 6, 27, 27, 27, 94, 157, 157, 157, 164, 164, 164, 164, 164, 1, 1, 1, 3, 3, 3, 3, 3, 6, 27, 27, 27, 94, 94, 157, 164, 1, 1, 1, 1] 167
rigid atoms, others: [1, 2, 3, 36, 37, 35, 19, 20, 21, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 587
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071062 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071062
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071062/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071062
Building REAL250005071063
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071063'
/scratch/stefan/7916153/working/building/REAL250005071063 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071063

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071063/0 /scratch/stefan/7916153/working/building/REAL250005071063 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 180)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/180
`/scratch/stefan/7916153/working/3D/180' -> `0.mol2'
Preparing input files

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

`REAL250005071063.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071063.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071063/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071063 none C#CC(C)(C)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', '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', '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, 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, 6, 7]
dock color type numbers: [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]
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, 112, 190, 190, 112, 112, 82, 35, 82, 80, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 190, 190, 190, 190, 190, 190, 190, 112, 82, 82, 82, 35, 35, 9, 1] 190
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])
total number of confs: 787
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071063 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071063
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071063/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071063
Building REAL250005071064
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071064'
/scratch/stefan/7916153/working/building/REAL250005071064 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071064

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071064/0 /scratch/stefan/7916153/working/building/REAL250005071064 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 181)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/181
`/scratch/stefan/7916153/working/3D/181' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CNC(=O)N1)

`REAL250005071064.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071064.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071064/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071064 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CNC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [23, 10, 23, 23, 70, 94, 94, 94, 100, 100, 100, 100, 100, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 70, 70, 94, 100, 10, 1, 1, 1, 1] 100
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 365
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071064 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CNC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [59, 22, 61, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 61, 88, 88, 88, 100, 100, 100, 100, 100, 100, 61, 61, 61, 22, 22, 8, 1, 88, 100, 100, 100, 100] 100
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 371
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071064 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071064
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071064/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071064
Building REAL250005071065
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071065'
/scratch/stefan/7916153/working/building/REAL250005071065 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL250005071065

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071065/0 /scratch/stefan/7916153/working/building/REAL250005071065 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 182)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/182
`/scratch/stefan/7916153/working/3D/182' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1CCC1C)

`REAL250005071065.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071065.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071065/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071065 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1CCC1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 64, 64, 151, 198, 198, 198, 201, 201, 201, 201, 201, 23, 5, 23, 1, 1, 1, 1, 1, 1, 64, 64, 64, 151, 151, 198, 201, 23, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2] 201
rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 779
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071065 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1CCC1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 80, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 80, 138, 138, 138, 198, 201, 201, 201, 201, 80, 80, 80, 22, 22, 8, 1, 138, 198, 198, 201, 201, 201, 201, 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, 38, 39])
total number of confs: 814
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071065 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071065/1 /scratch/stefan/7916153/working/building/REAL250005071065 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 183)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/183
`/scratch/stefan/7916153/working/3D/183' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@@H+]1CCC1C)

`REAL250005071065.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071065.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071065/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071065 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@@H+]1CCC1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [13, 10, 13, 13, 15, 15, 15, 15, 20, 20, 20, 20, 20, 10, 5, 10, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 15, 15, 15, 20, 10, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2] 20
rigid atoms, others: [33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 80
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071065 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@@H+]1CCC1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [16, 13, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 17, 17, 17, 20, 20, 20, 20, 20, 20, 16, 16, 16, 13, 13, 7, 1, 17, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 20
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 85
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071065 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `2'
/scratch/stefan/7916153/working/building/REAL250005071065/2 /scratch/stefan/7916153/working/building/REAL250005071065 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 2 (index: 184)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/184
`/scratch/stefan/7916153/working/3D/184' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@H+]1CCC1C)

`REAL250005071065.mol2' -> `2.mol2'
`temp.mol2' -> `REAL250005071065.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071065/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071065 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@H+]1CCC1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [5, 4, 5, 5, 6, 6, 6, 6, 8, 8, 8, 8, 8, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 8, 4, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2] 8
rigid atoms, others: [33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 35
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071065 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[N@H+]1CCC1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 6, 8, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 5, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 36
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071065 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071065
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
2: /scratch/stefan/7916153/working/building/REAL250005071065/2.*
1: /scratch/stefan/7916153/working/building/REAL250005071065/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071065/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071065
Building REAL250005071066
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071066'
/scratch/stefan/7916153/working/building/REAL250005071066 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071066

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071066/0 /scratch/stefan/7916153/working/building/REAL250005071066 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 185)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/185
`/scratch/stefan/7916153/working/3D/185' -> `0.mol2'
Preparing input files

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

`REAL250005071066.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071066.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071066/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071066 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C=CC[NH+](C)C 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [16, 14, 16, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 16, 23, 23, 23, 29, 29, 29, 29, 29, 29, 16, 16, 16, 14, 14, 10, 1, 23, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 29
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 105
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071066 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071066
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071066/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071066
Building REAL250005071067
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071067'
/scratch/stefan/7916153/working/building/REAL250005071067 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071067

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071067/0 /scratch/stefan/7916153/working/building/REAL250005071067 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 186)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/186
`/scratch/stefan/7916153/working/3D/186' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCSC1)

`REAL250005071067.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071067.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071067/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071067 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCSC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [40, 13, 40, 40, 95, 138, 138, 138, 144, 144, 144, 144, 144, 13, 1, 13, 1, 1, 1, 1, 1, 40, 40, 40, 95, 95, 138, 144, 13, 1, 1, 1, 1, 1] 144
rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 533
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071067 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCSC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [70, 27, 72, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 72, 109, 109, 109, 144, 144, 144, 144, 72, 72, 72, 27, 27, 10, 1, 109, 144, 144, 144, 144, 144] 144
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])
total number of confs: 461
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071067 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071067
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071067/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071067
Building REAL250005071068
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071068'
/scratch/stefan/7916153/working/building/REAL250005071068 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071068

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071068/0 /scratch/stefan/7916153/working/building/REAL250005071068 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 187)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/187
`/scratch/stefan/7916153/working/3D/187' -> `0.mol2'
Preparing input files

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

`REAL250005071068.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071068.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071068/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071068 none CO[C@H](C)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 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', '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, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [166, 163, 129, 164, 164, 129, 129, 82, 30, 82, 79, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 166, 166, 166, 164, 164, 164, 129, 82, 82, 82, 30, 30, 9, 1] 166
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: 664
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071068 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071068
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071068/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071068
Building REAL250005071069
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071069'
/scratch/stefan/7916153/working/building/REAL250005071069 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071069

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071069/0 /scratch/stefan/7916153/working/building/REAL250005071069 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 188)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/188
`/scratch/stefan/7916153/working/3D/188' -> `0.mol2'
Preparing input files

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

`REAL250005071069.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071069.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071069/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071069 none CC(=O)CCC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 5, 5, 1, 11, 8, 5, 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, 6, 7]
dock color type numbers: [7, 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]
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, 36, 40, 31, 14, 14, 14, 12, 9, 12, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 40, 40, 40, 36, 36, 31, 31, 14, 12, 12, 12, 9, 9, 5, 1] 40
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])
total number of confs: 168
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071069 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071069
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071069/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071069
Building REAL250005071070
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071070'
/scratch/stefan/7916153/working/building/REAL250005071070 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071070

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071070/0 /scratch/stefan/7916153/working/building/REAL250005071070 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 189)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/189
`/scratch/stefan/7916153/working/3D/189' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCC1O)

`REAL250005071070.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071070.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071070/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071070 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCC1O 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
225  conformations in input
total number of sets (complete confs): 225
using faster count positions algorithm for large data
unique positions, atoms: [16, 5, 16, 16, 53, 72, 72, 72, 75, 75, 75, 75, 75, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 16, 16, 53, 53, 72, 75, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3] 225
rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 16, 17, 18, 19, 20, 21, 30, 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, 38])
total number of confs: 273
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071070 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCCC1O 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
225  conformations in input
total number of sets (complete confs): 225
using faster count positions algorithm for large data
unique positions, atoms: [48, 20, 50, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 50, 71, 71, 71, 75, 75, 75, 75, 75, 50, 50, 50, 20, 20, 9, 1, 71, 75, 75, 75, 75, 75, 75, 75, 75, 225] 225
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: 505
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071070 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071070
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071070/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071070
Building REAL250005071071
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071071'
/scratch/stefan/7916153/working/building/REAL250005071071 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071071

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071071/0 /scratch/stefan/7916153/working/building/REAL250005071071 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 190)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/190
`/scratch/stefan/7916153/working/3D/190' -> `0.mol2'
Preparing input files

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

`REAL250005071071.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071071.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071071/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071071 none C[C@@H](O)C(=O)N[C@H](C)CNC(=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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 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]
1  hydrogens need rotated
375  conformations in input
total number of sets (complete confs): 375
using faster count positions algorithm for large data
unique positions, atoms: [125, 116, 125, 125, 116, 116, 83, 38, 83, 82, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 125, 125, 125, 375, 116, 83, 83, 83, 38, 38, 11, 1] 375
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])
total number of confs: 859
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071071 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071071
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071071/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071071
Building REAL250005071072
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071072'
/scratch/stefan/7916153/working/building/REAL250005071072 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071072

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071072/0 /scratch/stefan/7916153/working/building/REAL250005071072 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 191)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/191
`/scratch/stefan/7916153/working/3D/191' -> `0.mol2'
Preparing input files

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

`REAL250005071072.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071072.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071072/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071072 none CC[NH+](CC)CC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 1, 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
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, 16, 16, 16, 13, 7, 13, 13, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 13, 13, 13, 7, 7, 3, 1] 18
rigid atoms, others: [42, 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, 40, 41])
total number of confs: 73
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071072 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071072
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071072/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071072
Building REAL250005071073
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071073'
/scratch/stefan/7916153/working/building/REAL250005071073 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071073

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071073/0 /scratch/stefan/7916153/working/building/REAL250005071073 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 192)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/192
`/scratch/stefan/7916153/working/3D/192' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1CCC1)

`REAL250005071073.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071073.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071073/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071073 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 24, 59, 59, 138, 198, 198, 198, 201, 201, 201, 201, 201, 24, 6, 24, 1, 1, 1, 1, 1, 59, 59, 59, 138, 138, 198, 201, 24, 6, 6, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 765
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071073 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 77, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 77, 136, 136, 136, 193, 201, 201, 201, 77, 77, 77, 23, 23, 8, 1, 136, 193, 193, 201, 201, 201, 201, 201, 201] 201
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, 36])
total number of confs: 821
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071073 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071073/1 /scratch/stefan/7916153/working/building/REAL250005071073 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 193)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/193
`/scratch/stefan/7916153/working/3D/193' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[NH+]1CCC1)

`REAL250005071073.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071073.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071073/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071073 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[NH+]1CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [6, 5, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 5, 3, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 8, 5, 3, 3, 1, 1, 1, 1, 1, 1] 8
rigid atoms, others: [32, 33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 26
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071073 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C[NH+]1CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 9, 6, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 6, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 5, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8
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: 29
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071073 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071073
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071073/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071073/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071073
Building REAL250005071074
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071074'
/scratch/stefan/7916153/working/building/REAL250005071074 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071074

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071074/0 /scratch/stefan/7916153/working/building/REAL250005071074 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 194)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/194
`/scratch/stefan/7916153/working/3D/194' -> `0.mol2'
Preparing input files

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

`REAL250005071074.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071074.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071074/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071074 none CC(C)C(O)CC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 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]
1  hydrogens need rotated
582  conformations in input
total number of sets (complete confs): 582
using faster count positions algorithm for large data
unique positions, atoms: [194, 161, 194, 121, 161, 68, 68, 68, 43, 18, 43, 43, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 194, 194, 194, 161, 483, 121, 121, 68, 43, 43, 43, 18, 18, 5, 1] 582
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: 1417
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071074 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071074
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071074/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071074
Building REAL250005071075
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071075'
/scratch/stefan/7916153/working/building/REAL250005071075 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071075

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071075/0 /scratch/stefan/7916153/working/building/REAL250005071075 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 195)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/195
`/scratch/stefan/7916153/working/3D/195' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(=O)C1)

`REAL250005071075.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071075.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071075/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071075 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(=O)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
147  conformations in input
total number of sets (complete confs): 147
using faster count positions algorithm for large data
unique positions, atoms: [33, 10, 33, 33, 96, 137, 137, 137, 147, 147, 147, 147, 147, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 33, 33, 96, 96, 137, 147, 10, 1, 1, 1, 1, 1] 147
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 538
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071075 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1COC(=O)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
147  conformations in input
total number of sets (complete confs): 147
using faster count positions algorithm for large data
unique positions, atoms: [63, 25, 64, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 64, 94, 94, 94, 147, 147, 147, 147, 147, 64, 64, 64, 25, 25, 10, 1, 94, 147, 147, 147, 147, 147] 147
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])
total number of confs: 539
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071075 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071075
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071075/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071075
Building REAL250005071076
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071076'
/scratch/stefan/7916153/working/building/REAL250005071076 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071076

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071076/0 /scratch/stefan/7916153/working/building/REAL250005071076 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 196)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/196
`/scratch/stefan/7916153/working/3D/196' -> `0.mol2'
Preparing input files

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

`REAL250005071076.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071076.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071076/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071076 none CC(O)C(C)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.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', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 4, 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]
1  hydrogens need rotated
492  conformations in input
total number of sets (complete confs): 492
using faster count positions algorithm for large data
unique positions, atoms: [164, 151, 164, 93, 151, 93, 93, 66, 24, 66, 64, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 492, 151, 151, 151, 151, 93, 66, 66, 66, 24, 24, 9, 1] 492
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: 1178
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071076 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071076
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071076/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071076
Building REAL250005071077
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071077'
/scratch/stefan/7916153/working/building/REAL250005071077 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071077

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071077/0 /scratch/stefan/7916153/working/building/REAL250005071077 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 197)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/197
`/scratch/stefan/7916153/working/3D/197' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CCOC1)

`REAL250005071077.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071077.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071077/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071077 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CCOC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 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
525  conformations in input
total number of sets (complete confs): 525
using faster count positions algorithm for large data
unique positions, atoms: [34, 8, 34, 34, 108, 163, 163, 163, 175, 175, 175, 175, 175, 8, 1, 8, 1, 1, 1, 1, 1, 1, 34, 34, 34, 108, 108, 163, 175, 8, 6, 1, 1, 1, 1, 1, 1] 525
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 630
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071077 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CCOC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 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
525  conformations in input
total number of sets (complete confs): 525
using faster count positions algorithm for large data
unique positions, atoms: [92, 37, 94, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 94, 137, 137, 137, 175, 175, 175, 175, 175, 94, 94, 94, 37, 37, 10, 1, 137, 525, 175, 175, 175, 175, 175, 175] 525
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])
total number of confs: 1179
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071077 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071077
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071077/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071077
Building REAL250005071078
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071078'
/scratch/stefan/7916153/working/building/REAL250005071078 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071078

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071078/0 /scratch/stefan/7916153/working/building/REAL250005071078 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 198)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/198
`/scratch/stefan/7916153/working/3D/198' -> `0.mol2'
Preparing input files

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

`REAL250005071078.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071078.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071078/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071078 none CCC(C)(C#N)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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]
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: [111, 109, 69, 109, 109, 109, 69, 69, 42, 19, 42, 42, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 109, 109, 109, 69, 42, 42, 42, 19, 19, 7, 1] 115
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: 509
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071078 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071078
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071078/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071078
Building REAL250005071079
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071079'
/scratch/stefan/7916153/working/building/REAL250005071079 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071079

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071079/0 /scratch/stefan/7916153/working/building/REAL250005071079 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 199)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/199
`/scratch/stefan/7916153/working/3D/199' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005071079.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071079.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071079/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071079 none C=C1CC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 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', '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, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 111, 111, 111, 75, 29, 75, 73, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 111, 75, 75, 75, 29, 29, 9, 1] 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])
total number of confs: 688
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071079 none C=C1CC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 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', '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, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 145, 192, 192, 192, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 13, 54, 54, 54, 145, 145, 192, 201] 201
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])
total number of confs: 746
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071079 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071079
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071079/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071079
Building REAL250005071080
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071080'
/scratch/stefan/7916153/working/building/REAL250005071080 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071080

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071080/0 /scratch/stefan/7916153/working/building/REAL250005071080 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 200)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/200
`/scratch/stefan/7916153/working/3D/200' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC=CC1)

`REAL250005071080.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071080.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071080/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071080 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC=CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 92, 92, 159, 201, 201, 201, 201, 201, 201, 201, 201, 38, 6, 38, 1, 1, 1, 1, 1, 1, 92, 92, 92, 159, 159, 201, 201, 38, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 816
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071080 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC=CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 48, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 48, 70, 70, 70, 183, 201, 201, 201, 201, 48, 48, 48, 18, 18, 4, 1, 70, 183, 183, 201, 201, 201, 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, 38])
total number of confs: 813
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071080 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071080
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071080/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071080
Building REAL250005071081
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071081'
/scratch/stefan/7916153/working/building/REAL250005071081 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071081

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071081/0 /scratch/stefan/7916153/working/building/REAL250005071081 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 201)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/201
`/scratch/stefan/7916153/working/3D/201' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1OCCO1)

`REAL250005071081.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071081.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071081/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071081 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1OCCO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [89, 39, 89, 89, 166, 201, 201, 201, 201, 201, 201, 201, 201, 39, 10, 39, 1, 1, 1, 1, 1, 1, 89, 89, 89, 166, 166, 201, 201, 39, 10, 10, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 806
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071081 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1OCCO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 20, 60, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 60, 91, 91, 91, 166, 201, 201, 201, 201, 60, 60, 60, 20, 20, 6, 1, 91, 166, 166, 201, 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])
total number of confs: 797
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071081 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071081
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071081/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071081
Building REAL250005071082
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071082'
/scratch/stefan/7916153/working/building/REAL250005071082 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071082

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071082/0 /scratch/stefan/7916153/working/building/REAL250005071082 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 202)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/202
`/scratch/stefan/7916153/working/3D/202' -> `0.mol2'
Preparing input files

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

`REAL250005071082.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071082.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071082/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071082 none COC(OC)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 12, 5, 1, 11, 8, 5, 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, 6, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens 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, 160, 84, 160, 193, 84, 84, 48, 15, 48, 46, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 200, 200, 160, 193, 193, 193, 84, 48, 48, 48, 15, 15, 4, 1] 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])
total number of confs: 798
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071082 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071082
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071082/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071082
Building REAL250005071083
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071083'
/scratch/stefan/7916153/working/building/REAL250005071083 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071083

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071083/0 /scratch/stefan/7916153/working/building/REAL250005071083 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 203)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/203
`/scratch/stefan/7916153/working/3D/203' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(C#N)CC1)

`REAL250005071083.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071083.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071083/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071083 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(C#N)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 29, 69, 69, 138, 184, 184, 184, 201, 201, 201, 201, 201, 29, 5, 29, 1, 1, 1, 1, 1, 1, 69, 69, 69, 138, 138, 184, 201, 29, 5, 5, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 750
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071083 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(C#N)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 61, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 61, 97, 97, 97, 184, 201, 201, 201, 201, 61, 61, 61, 24, 24, 9, 1, 97, 184, 184, 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])
total number of confs: 824
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071083 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071083
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071083/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071083
Building REAL250005071084
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071084'
/scratch/stefan/7916153/working/building/REAL250005071084 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071084

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071084/0 /scratch/stefan/7916153/working/building/REAL250005071084 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 204)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/204
`/scratch/stefan/7916153/working/3D/204' -> `0.mol2'
Preparing input files

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

`REAL250005071084.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071084.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071084/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071084 none COC(=O)CCC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 1, 11, 8, 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, 6, 7]
dock color type numbers: [7, 3, 7, 5, 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
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, 126, 56, 56, 56, 36, 16, 36, 36, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 149, 149, 126, 126, 56, 36, 36, 36, 16, 16, 4, 1] 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])
total number of confs: 832
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071084 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071084
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071084/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071084
Building REAL250005071085
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071085'
/scratch/stefan/7916153/working/building/REAL250005071085 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071085

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071085/0 /scratch/stefan/7916153/working/building/REAL250005071085 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 205)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/205
`/scratch/stefan/7916153/working/3D/205' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCOC1)

`REAL250005071085.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071085.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071085/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071085 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCOC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
170  conformations in input
total number of sets (complete confs): 170
using faster count positions algorithm for large data
unique positions, atoms: [43, 11, 43, 43, 115, 159, 159, 159, 170, 170, 170, 170, 170, 11, 1, 11, 1, 1, 1, 1, 1, 1, 43, 43, 43, 115, 115, 159, 170, 11, 1, 1, 1, 1, 1, 1, 1] 170
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 631
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071085 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCOC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
170  conformations in input
total number of sets (complete confs): 170
using faster count positions algorithm for large data
unique positions, atoms: [66, 27, 68, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 68, 107, 107, 107, 170, 170, 170, 170, 170, 68, 68, 68, 27, 27, 9, 1, 107, 170, 170, 170, 170, 170, 170, 170] 170
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])
total number of confs: 502
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071085 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071085
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071085/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071085
Building REAL250005071086
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071086'
/scratch/stefan/7916153/working/building/REAL250005071086 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071086

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071086/0 /scratch/stefan/7916153/working/building/REAL250005071086 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 206)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/206
`/scratch/stefan/7916153/working/3D/206' -> `0.mol2'
Preparing input files

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

`REAL250005071086.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071086.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071086/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071086 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(O)C(C)(C)C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [66, 31, 68, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 68, 87, 87, 87, 94, 94, 94, 94, 94, 68, 68, 68, 31, 31, 11, 1, 87, 94, 282, 94, 94, 94, 94, 94, 94, 94, 94, 94] 282
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, 39, 40])
total number of confs: 655
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071086 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071086
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071086/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071086
Building REAL250005071087
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071087'
/scratch/stefan/7916153/working/building/REAL250005071087 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071087

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071087/0 /scratch/stefan/7916153/working/building/REAL250005071087 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 207)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/207
`/scratch/stefan/7916153/working/3D/207' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)COC1)

`REAL250005071087.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071087.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071087/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071087 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)COC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [29, 6, 29, 29, 95, 139, 139, 139, 150, 150, 150, 150, 150, 6, 1, 6, 1, 1, 1, 1, 1, 29, 29, 29, 95, 95, 139, 150, 6, 2, 2, 2, 1, 1, 1, 1] 150
rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 535
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071087 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)COC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [59, 25, 60, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 60, 79, 79, 79, 150, 150, 150, 150, 60, 60, 60, 25, 25, 9, 1, 79, 150, 150, 150, 150, 150, 150, 150] 150
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: 511
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071087 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071087
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071087/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071087
Building REAL250005071088
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071088'
/scratch/stefan/7916153/working/building/REAL250005071088 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071088

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071088/0 /scratch/stefan/7916153/working/building/REAL250005071088 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 208)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/208
`/scratch/stefan/7916153/working/3D/208' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCCO1)

`REAL250005071088.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071088.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071088/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071088 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCCO1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [21, 8, 21, 21, 56, 89, 89, 89, 98, 98, 98, 98, 98, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 56, 56, 89, 98, 8, 1, 1, 1, 1, 1, 1, 1] 98
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 335
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071088 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCCO1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [63, 31, 63, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 63, 90, 90, 90, 98, 98, 98, 98, 98, 63, 63, 63, 31, 31, 11, 1, 90, 98, 98, 98, 98, 98, 98, 98] 98
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])
total number of confs: 343
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071088 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071088
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071088/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071088
Building REAL250005071089
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071089'
/scratch/stefan/7916153/working/building/REAL250005071089 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071089

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071089/0 /scratch/stefan/7916153/working/building/REAL250005071089 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 209)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/209
`/scratch/stefan/7916153/working/3D/209' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CCCO1)

`REAL250005071089.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071089.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071089/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071089 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CCCO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [33, 8, 33, 33, 96, 151, 151, 151, 162, 162, 162, 162, 162, 8, 1, 8, 1, 1, 1, 1, 1, 1, 33, 33, 33, 96, 96, 151, 162, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1] 162
rigid atoms, others: [33, 34, 35, 36, 37, 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])
total number of confs: 576
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071089 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CCCO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [86, 35, 88, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 88, 132, 132, 132, 162, 162, 162, 162, 162, 88, 88, 88, 35, 35, 11, 1, 132, 162, 162, 162, 162, 162, 162, 162, 162, 162] 162
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: 610
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071089 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071089
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071089/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071089
Building REAL250005071090
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071090'
/scratch/stefan/7916153/working/building/REAL250005071090 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071090

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071090/0 /scratch/stefan/7916153/working/building/REAL250005071090 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 210)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/210
`/scratch/stefan/7916153/working/3D/210' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(=O)N1)

`REAL250005071090.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071090.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071090/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071090 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 6, 4, 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: [32, 11, 32, 32, 71, 92, 92, 92, 96, 96, 96, 96, 96, 11, 1, 11, 1, 1, 1, 1, 1, 32, 32, 32, 71, 71, 92, 96, 11, 1, 1, 1, 1] 96
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 366
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071090 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 6, 4, 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: [55, 23, 56, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 56, 74, 74, 74, 96, 96, 96, 96, 56, 56, 56, 23, 23, 9, 1, 74, 96, 96, 96, 96] 96
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])
total number of confs: 347
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071090 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071090
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071090/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071090
Building REAL250005071091
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071091'
/scratch/stefan/7916153/working/building/REAL250005071091 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071091

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071091/0 /scratch/stefan/7916153/working/building/REAL250005071091 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 211)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/211
`/scratch/stefan/7916153/working/3D/211' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC(=O)N1)

`REAL250005071091.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071091.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071091/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071091 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 6, 4, 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: [31, 11, 31, 31, 80, 113, 113, 113, 121, 121, 121, 121, 121, 11, 1, 11, 1, 1, 1, 1, 1, 1, 31, 31, 31, 80, 80, 113, 121, 11, 1, 1, 1] 121
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 452
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071091 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@@H]1CC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 6, 4, 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: [56, 23, 58, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 58, 91, 91, 91, 121, 121, 121, 121, 121, 58, 58, 58, 23, 23, 10, 1, 91, 121, 121, 121] 121
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])
total number of confs: 433
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071091 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071091
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071091/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071091
Building REAL250005071092
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071092'
/scratch/stefan/7916153/working/building/REAL250005071092 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071092

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071092/0 /scratch/stefan/7916153/working/building/REAL250005071092 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 212)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/212
`/scratch/stefan/7916153/working/3D/212' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCCC1)

`REAL250005071092.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071092.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071092/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071092 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCCC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [41, 10, 41, 41, 104, 149, 149, 149, 161, 161, 161, 161, 161, 10, 1, 10, 1, 1, 1, 1, 1, 1, 41, 41, 41, 104, 104, 149, 161, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1] 161
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 587
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071092 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CCCCC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [73, 31, 75, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 75, 106, 106, 106, 161, 161, 161, 161, 161, 75, 75, 75, 31, 31, 10, 1, 106, 161, 161, 161, 161, 161, 161, 161, 161, 161] 161
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: 507
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071092 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071092
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071092/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071092
Building REAL250005071093
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071093'
/scratch/stefan/7916153/working/building/REAL250005071093 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071093

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071093/0 /scratch/stefan/7916153/working/building/REAL250005071093 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 213)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/213
`/scratch/stefan/7916153/working/3D/213' -> `0.mol2'
Preparing input files

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

`REAL250005071093.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071093.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071093/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071093 none CCC[C@H](O)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 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', '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, 5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 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, 191, 149, 93, 149, 149, 93, 93, 57, 20, 57, 55, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 199, 193, 193, 447, 93, 57, 57, 57, 20, 20, 4, 1] 603
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: 1384
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071093 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071093
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071093/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071093
Building REAL250005071094
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071094'
/scratch/stefan/7916153/working/building/REAL250005071094 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071094

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071094/0 /scratch/stefan/7916153/working/building/REAL250005071094 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 214)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/214
`/scratch/stefan/7916153/working/3D/214' -> `0.mol2'
Preparing input files

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

`REAL250005071094.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071094.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071094/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071094 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC(C)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 6, 33, 33, 115, 193, 193, 193, 201, 201, 201, 201, 201, 6, 1, 6, 1, 1, 1, 1, 1, 1, 33, 33, 33, 115, 115, 193, 201, 6, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1] 201
rigid atoms, others: [33, 34, 35, 39, 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, 36, 37, 38])
total number of confs: 726
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071094 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC(C)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 75, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 75, 115, 115, 115, 201, 201, 201, 201, 201, 75, 75, 75, 26, 26, 8, 1, 115, 201, 201, 201, 201, 201, 201, 201, 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, 38, 39, 40])
total number of confs: 695
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071094 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071094
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071094/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071094
Building REAL250005071095
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071095'
/scratch/stefan/7916153/working/building/REAL250005071095 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071095

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071095/0 /scratch/stefan/7916153/working/building/REAL250005071095 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 215)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/215
`/scratch/stefan/7916153/working/3D/215' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)N1CCC1)

`REAL250005071095.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071095.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071095/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071095 none CC(C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)N1CCC1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 10, 5, 5, 5, 7, 7, 7, 7, 6, 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, 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: [3, 1, 3, 9, 9, 9, 36, 36, 36, 82, 124, 124, 124, 125, 125, 125, 125, 125, 1, 1, 1, 1, 3, 3, 3, 3, 9, 36, 36, 36, 82, 82, 124, 125, 1, 1, 1, 1, 1, 1] 125
rigid atoms, others: [1, 34, 35, 36, 37, 38, 39, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 475
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071095 none CC(C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)N1CCC1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 10, 5, 5, 5, 7, 7, 7, 7, 6, 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, 7]
0  hydrogens need rotated
125  conformations in input
total number of sets (complete confs): 125
using faster count positions algorithm for large data
unique positions, atoms: [125, 117, 117, 117, 79, 24, 79, 78, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 125, 125, 125, 125, 117, 79, 79, 79, 24, 24, 6, 1, 125, 125, 125, 125, 125, 125] 125
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, 38, 39])
total number of confs: 471
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071095 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071095/1 /scratch/stefan/7916153/working/building/REAL250005071095 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 216)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/216
`/scratch/stefan/7916153/working/3D/216' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)[NH+]1CCC1)

`REAL250005071095.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071095.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071095/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071095 none CC(C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)[NH+]1CCC1 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', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 5, 7, 7, 7, 7, 6, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 4, 4, 4, 5, 5, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 5, 5, 5, 6, 6, 8, 8, 1, 1, 1, 1, 1, 1] 8
rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 34
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071095 none CC(C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)[NH+]1CCC1 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', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 5, 7, 7, 7, 7, 6, 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, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 8, 8, 8, 7, 8, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 4, 1, 8, 8, 8, 8, 8, 8] 8
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, 39, 40])
total number of confs: 30
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071095 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071095
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071095/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071095/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071095
Building REAL250005071096
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071096'
/scratch/stefan/7916153/working/building/REAL250005071096 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071096

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071096/0 /scratch/stefan/7916153/working/building/REAL250005071096 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 217)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/217
`/scratch/stefan/7916153/working/3D/217' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CC1(F)F)

`REAL250005071096.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071096.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071096/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071096 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CC1(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [50, 13, 50, 50, 138, 193, 193, 193, 201, 201, 201, 201, 201, 13, 1, 13, 1, 1, 1, 1, 1, 1, 50, 50, 50, 138, 138, 193, 201, 13, 1, 1] 201
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 747
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071096 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CC1(F)F 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [77, 28, 79, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 79, 121, 121, 121, 201, 201, 201, 201, 201, 79, 79, 79, 27, 27, 10, 1, 121, 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])
total number of confs: 717
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071096 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071096
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071096/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071096
Building REAL250005071097
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071097'
/scratch/stefan/7916153/working/building/REAL250005071097 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071097

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071097/0 /scratch/stefan/7916153/working/building/REAL250005071097 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 218)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/218
`/scratch/stefan/7916153/working/3D/218' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CNN=C1)

`REAL250005071097.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071097.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071097/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071097 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CNN=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 20, 60, 60, 129, 193, 193, 193, 201, 201, 201, 201, 201, 20, 7, 20, 1, 1, 1, 1, 1, 1, 60, 60, 60, 129, 129, 193, 201, 20, 7, 7, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 779
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071097 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CNN=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [65, 27, 65, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 65, 121, 121, 121, 183, 188, 188, 188, 188, 65, 65, 65, 27, 27, 9, 1, 121, 183, 183, 188, 188, 188] 188
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])
total number of confs: 725
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071097 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071097
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071097/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071097
Building REAL250005071098
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071098'
/scratch/stefan/7916153/working/building/REAL250005071098 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071098

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071098/0 /scratch/stefan/7916153/working/building/REAL250005071098 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 219)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/219
`/scratch/stefan/7916153/working/3D/219' -> `0.mol2'
Preparing input files

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

`REAL250005071098.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071098.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071098/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071098 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC(=O)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [30, 7, 30, 30, 106, 162, 162, 162, 178, 178, 178, 178, 178, 7, 1, 7, 1, 1, 1, 1, 1, 1, 30, 30, 30, 106, 106, 162, 178, 7, 2, 2, 2, 1, 1, 1, 1] 178
rigid atoms, others: [33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 621
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071098 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(C)CC(=O)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [71, 28, 72, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 72, 96, 96, 96, 178, 178, 178, 178, 178, 72, 72, 72, 28, 28, 10, 1, 96, 178, 178, 178, 178, 178, 178, 178] 178
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])
total number of confs: 608
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071098 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071098
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071098/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071098
Building REAL250005071099
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071099'
/scratch/stefan/7916153/working/building/REAL250005071099 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071099

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071099/0 /scratch/stefan/7916153/working/building/REAL250005071099 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 220)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/220
`/scratch/stefan/7916153/working/3D/220' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CNC=C1)

`REAL250005071099.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071099.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071099/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071099 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CNC=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 19, 63, 63, 131, 200, 200, 200, 201, 201, 201, 201, 201, 19, 7, 19, 1, 1, 1, 1, 1, 1, 63, 63, 63, 131, 131, 200, 201, 19, 7, 7, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 802
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071099 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1=CNC=C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 15, 38, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 38, 72, 72, 72, 126, 201, 201, 201, 201, 38, 38, 38, 15, 15, 5, 1, 72, 126, 126, 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])
total number of confs: 665
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071099 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071099
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071099/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071099
Building REAL250005071100
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071100'
/scratch/stefan/7916153/working/building/REAL250005071100 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071100

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071100/0 /scratch/stefan/7916153/working/building/REAL250005071100 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 221)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/221
`/scratch/stefan/7916153/working/3D/221' -> `0.mol2'
Preparing input files

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

`REAL250005071100.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071100.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071100/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071100 none CCCC(C)(O)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 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, 200, 143, 107, 143, 143, 107, 107, 64, 25, 64, 62, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 143, 143, 143, 429, 107, 64, 64, 64, 25, 25, 6, 1] 603
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: 1341
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071100 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071100
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071100/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071100
Building REAL250005071101
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071101'
/scratch/stefan/7916153/working/building/REAL250005071101 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071101

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071101/0 /scratch/stefan/7916153/working/building/REAL250005071101 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 222)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/222
`/scratch/stefan/7916153/working/3D/222' -> `0.mol2'
Preparing input files

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

`REAL250005071101.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071101.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071101/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071101 none CCOC(C)(C)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 190, 122, 190, 190, 122, 122, 68, 21, 68, 66, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 190, 190, 190, 190, 190, 190, 122, 68, 68, 68, 21, 21, 4, 1] 201
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: 821
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071101 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071101
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071101/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071101
Building REAL250005071102
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071102'
/scratch/stefan/7916153/working/building/REAL250005071102 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071102

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071102/0 /scratch/stefan/7916153/working/building/REAL250005071102 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 223)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/223
`/scratch/stefan/7916153/working/3D/223' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(=O)C1)

`REAL250005071102.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071102.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071102/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071102 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(=O)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [86, 37, 86, 86, 167, 201, 201, 201, 201, 201, 201, 201, 201, 37, 6, 37, 1, 1, 1, 1, 1, 1, 86, 86, 86, 167, 167, 201, 201, 37, 6, 6, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 806
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071102 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CC(=O)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [57, 20, 57, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 57, 92, 92, 92, 161, 201, 201, 201, 201, 57, 57, 57, 20, 20, 5, 1, 92, 161, 161, 201, 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])
total number of confs: 837
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071102 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071102
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071102/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071102
Building REAL250005071103
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071103'
/scratch/stefan/7916153/working/building/REAL250005071103 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071103

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071103/0 /scratch/stefan/7916153/working/building/REAL250005071103 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 224)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/224
`/scratch/stefan/7916153/working/3D/224' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CSC1)

`REAL250005071103.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071103.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071103/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071103 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CSC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [96, 41, 96, 96, 164, 198, 198, 198, 201, 201, 201, 201, 201, 41, 8, 41, 1, 1, 1, 1, 1, 96, 96, 96, 164, 164, 198, 201, 41, 8, 8, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 790
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071103 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1CSC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 59, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 59, 98, 98, 98, 168, 201, 201, 201, 59, 59, 59, 22, 22, 7, 1, 98, 168, 168, 201, 201, 201, 201, 201] 201
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: 849
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071103 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071103
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071103/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071103
Building REAL250005071104
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071104'
/scratch/stefan/7916153/working/building/REAL250005071104 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071104

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071104/0 /scratch/stefan/7916153/working/building/REAL250005071104 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 225)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/225
`/scratch/stefan/7916153/working/3D/225' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(F)CCC1)

`REAL250005071104.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071104.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071104/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071104 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(F)CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [35, 10, 35, 35, 97, 145, 145, 145, 150, 150, 150, 150, 150, 10, 1, 10, 1, 1, 1, 1, 1, 35, 35, 35, 97, 97, 145, 150, 10, 1, 1, 1, 1, 1, 1] 150
rigid atoms, others: [32, 33, 34, 14, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 549
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071104 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(F)CCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 15, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [68, 32, 70, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 70, 110, 110, 110, 150, 150, 150, 150, 70, 70, 70, 32, 32, 10, 1, 110, 150, 150, 150, 150, 150, 150] 150
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])
total number of confs: 542
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071104 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071104
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071104/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071104
Building REAL250005071105
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071105'
/scratch/stefan/7916153/working/building/REAL250005071105 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071105

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071105/0 /scratch/stefan/7916153/working/building/REAL250005071105 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 226)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/226
`/scratch/stefan/7916153/working/3D/226' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=CN1)

`REAL250005071105.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071105.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071105/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071105 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=CN1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [23, 7, 23, 23, 50, 69, 69, 69, 72, 72, 72, 72, 72, 7, 1, 7, 1, 1, 1, 1, 1, 23, 23, 23, 50, 50, 69, 72, 7, 1, 1, 1] 72
rigid atoms, others: [14, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 261
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071105 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=CN1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 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: [48, 18, 49, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 49, 65, 65, 65, 72, 72, 72, 72, 49, 49, 49, 18, 18, 8, 1, 65, 72, 72, 72] 72
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])
total number of confs: 255
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071105 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071105
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071105/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071105
Building REAL250005071106
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071106'
/scratch/stefan/7916153/working/building/REAL250005071106 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071106

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071106/0 /scratch/stefan/7916153/working/building/REAL250005071106 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 227)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/227
`/scratch/stefan/7916153/working/3D/227' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)=N1)

`REAL250005071106.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071106.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071106/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071106 none CC1=NOC(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [113, 113, 113, 113, 96, 96, 96, 61, 27, 61, 61, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 96, 61, 61, 61, 27, 27, 8, 1] 113
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])
total number of confs: 392
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071106 none CC1=NOC(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 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]
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: [1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 21, 63, 109, 109, 109, 113, 113, 113, 113, 113, 1, 2, 2, 2, 7, 21, 21, 21, 63, 63, 109, 113] 113
rigid atoms, others: [0, 1, 2, 3, 4, 5, 21] set([6, 7, 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: 411
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071106 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071106
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071106/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071106
Building REAL250005071107
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071107'
/scratch/stefan/7916153/working/building/REAL250005071107 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071107

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071107/0 /scratch/stefan/7916153/working/building/REAL250005071107 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 228)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/228
`/scratch/stefan/7916153/working/3D/228' -> `0.mol2'
Preparing input files

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

`REAL250005071107.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071107.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071107/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071107 none CCOC(=O)CC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 1, 11, 5, 1, 11, 8, 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, 6, 7]
dock color type numbers: [7, 7, 3, 7, 5, 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
133  conformations in input
total number of sets (complete confs): 133
using faster count positions algorithm for large data
unique positions, atoms: [133, 130, 130, 53, 130, 35, 35, 35, 23, 14, 23, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 53, 53, 35, 23, 23, 23, 14, 14, 4, 1] 133
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])
total number of confs: 465
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071107 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071107
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071107/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071107
Building REAL250005071108
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071108'
/scratch/stefan/7916153/working/building/REAL250005071108 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071108

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071108/0 /scratch/stefan/7916153/working/building/REAL250005071108 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 229)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/229
`/scratch/stefan/7916153/working/3D/229' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(=O)C1)

`REAL250005071108.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071108.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071108/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071108 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(=O)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [44, 12, 44, 44, 115, 166, 166, 166, 180, 180, 180, 180, 180, 12, 1, 12, 1, 1, 1, 1, 1, 44, 44, 44, 115, 115, 166, 180, 12, 1, 1, 1, 1, 1] 180
rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 643
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071108 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CC(=O)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [76, 33, 77, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 77, 106, 106, 106, 180, 180, 180, 180, 77, 77, 77, 33, 33, 13, 1, 106, 180, 180, 180, 180, 180] 180
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])
total number of confs: 641
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071108 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071108
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071108/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071108
Building REAL250005071109
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071109'
/scratch/stefan/7916153/working/building/REAL250005071109 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071109

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071109/0 /scratch/stefan/7916153/working/building/REAL250005071109 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 230)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/230
`/scratch/stefan/7916153/working/3D/230' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=CN=N1)

`REAL250005071109.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071109.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071109/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071109 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=CN=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [90, 46, 90, 90, 151, 190, 190, 190, 201, 201, 201, 201, 201, 46, 9, 46, 1, 1, 1, 1, 1, 1, 90, 90, 90, 151, 151, 190, 201, 46, 9, 9, 1, 1] 201
rigid atoms, others: [32, 33, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 792
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071109 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=CN=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 1, 8, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [55, 26, 55, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 55, 85, 85, 85, 172, 201, 201, 201, 201, 55, 55, 55, 26, 26, 9, 1, 85, 172, 172, 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])
total number of confs: 749
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071109 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071109
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071109/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071109
Building REAL250005071110
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071110'
/scratch/stefan/7916153/working/building/REAL250005071110 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071110

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071110/0 /scratch/stefan/7916153/working/building/REAL250005071110 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 231)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/231
`/scratch/stefan/7916153/working/3D/231' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CCC1)

`REAL250005071110.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071110.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071110/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071110 none C=CC1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CCC1 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', 'C.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, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 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, 100, 100, 100, 62, 20, 62, 61, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 100, 62, 62, 62, 20, 20, 4, 1, 201, 201, 201, 201, 201, 201] 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, 37, 38])
total number of confs: 682
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071110 none C=CC1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CCC1 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', 'C.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, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 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: [5, 1, 1, 1, 7, 7, 7, 30, 30, 30, 99, 187, 189, 187, 201, 201, 201, 201, 201, 1, 1, 1, 5, 5, 5, 7, 30, 30, 30, 99, 99, 189, 201, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 2, 3, 36, 37, 35, 33, 34, 19, 20, 21, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 692
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071110 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071110
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071110/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071110
Building REAL250005071111
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071111'
/scratch/stefan/7916153/working/building/REAL250005071111 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071111

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071111/0 /scratch/stefan/7916153/working/building/REAL250005071111 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 232)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/232
`/scratch/stefan/7916153/working/3D/232' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)COC1)

`REAL250005071111.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071111.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071111/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071111 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)COC1 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', 'N.am', 'C.2', 'O.2', 'C.3', '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: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 7, 3, 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: [32, 11, 32, 32, 72, 104, 104, 104, 111, 111, 111, 111, 111, 11, 1, 11, 1, 1, 1, 1, 1, 32, 32, 32, 72, 72, 104, 111, 11, 6, 1, 1, 1, 1] 333
rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 406
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071111 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)COC1 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', 'N.am', 'C.2', 'O.2', 'C.3', '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: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 7, 3, 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: [55, 24, 57, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 57, 78, 78, 78, 111, 111, 111, 111, 57, 57, 57, 24, 24, 10, 1, 78, 333, 111, 111, 111, 111] 333
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])
total number of confs: 740
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071111 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071111
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071111/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071111
Building REAL250005071112
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071112'
/scratch/stefan/7916153/working/building/REAL250005071112 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071112

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071112/0 /scratch/stefan/7916153/working/building/REAL250005071112 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 233)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/233
`/scratch/stefan/7916153/working/3D/233' -> `0.mol2'
Preparing input files

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

`REAL250005071112.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071112.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071112/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071112 none CCC(C)C(O)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 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, 198, 139, 198, 104, 139, 104, 104, 63, 20, 63, 61, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 198, 198, 198, 198, 139, 417, 104, 63, 63, 63, 20, 20, 5, 1] 603
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: 1316
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071112 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071112
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071112/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071112
Building REAL250005071113
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071113'
/scratch/stefan/7916153/working/building/REAL250005071113 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071113

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071113/0 /scratch/stefan/7916153/working/building/REAL250005071113 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 234)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/234
`/scratch/stefan/7916153/working/3D/234' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)=C1CC1)

`REAL250005071113.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071113.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071113/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071113 none CC(C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)=C1CC1 NO_LONG_NAME
dock atom types: ['C.3', '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.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 12, 12, 12, 49, 49, 49, 131, 186, 187, 186, 196, 196, 196, 196, 196, 1, 1, 1, 2, 2, 2, 12, 49, 49, 49, 131, 131, 187, 196, 1, 1, 1, 1] 196
rigid atoms, others: [0, 1, 2, 35, 33, 32, 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])
total number of confs: 740
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071113 none CC(C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)=C1CC1 NO_LONG_NAME
dock atom types: ['C.3', '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.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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]
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, 122, 122, 122, 77, 33, 77, 74, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 196, 196, 196, 196, 196, 196, 122, 77, 77, 77, 33, 33, 9, 1, 196, 196, 196, 196] 196
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: 681
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071113 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071113
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071113/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071113
Building REAL250005071114
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071114'
/scratch/stefan/7916153/working/building/REAL250005071114 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071114

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071114/0 /scratch/stefan/7916153/working/building/REAL250005071114 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 235)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/235
`/scratch/stefan/7916153/working/3D/235' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005071114.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071114.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071114/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071114 none CC1=CC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 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', '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, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 105, 105, 105, 72, 27, 72, 70, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 105, 72, 72, 72, 27, 27, 8, 1] 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])
total number of confs: 697
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071114 none CC1=CC1C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 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', '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, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 60, 60, 60, 150, 195, 195, 195, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 13, 60, 60, 60, 150, 150, 195, 201] 201
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])
total number of confs: 763
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071114 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071114
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071114/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071114
Building REAL250005071115
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071115'
/scratch/stefan/7916153/working/building/REAL250005071115 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071115

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071115/0 /scratch/stefan/7916153/working/building/REAL250005071115 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 236)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/236
`/scratch/stefan/7916153/working/3D/236' -> `0.mol2'
Preparing input files

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

`REAL250005071115.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071115.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071115/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071115 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C(=O)N(C)C 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', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [52, 20, 54, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 54, 77, 77, 77, 91, 91, 91, 91, 54, 54, 54, 20, 20, 6, 1, 77, 91, 91, 91, 91, 91, 91] 91
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])
total number of confs: 333
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071115 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071115
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071115/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071115
Building REAL250005071116
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071116'
/scratch/stefan/7916153/working/building/REAL250005071116 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071116

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071116/0 /scratch/stefan/7916153/working/building/REAL250005071116 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 237)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/237
`/scratch/stefan/7916153/working/3D/237' -> `0.mol2'
Preparing input files

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

`REAL250005071116.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071116.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071116/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071116 none CC(=O)C1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 176, 201, 86, 86, 86, 47, 16, 47, 46, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 176, 176, 201, 201, 201, 86, 47, 47, 47, 16, 16, 4, 1, 176, 176, 176, 176] 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])
total number of confs: 679
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071116 none CC(=O)C1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 1, 1, 7, 7, 7, 29, 29, 29, 97, 172, 172, 172, 176, 176, 176, 176, 176, 1, 1, 5, 5, 5, 7, 29, 29, 29, 97, 97, 172, 176, 1, 1, 1, 1] 201
rigid atoms, others: [1, 34, 3, 4, 33, 35, 20, 21, 36] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 631
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071116 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071116
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071116/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071116
Building REAL250005071117
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071117'
/scratch/stefan/7916153/working/building/REAL250005071117 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071117

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071117/0 /scratch/stefan/7916153/working/building/REAL250005071117 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 238)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/238
`/scratch/stefan/7916153/working/3D/238' -> `0.mol2'
Preparing input files

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

`REAL250005071117.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071117.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071117/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071117 none CCCC(O)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 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, 199, 136, 105, 136, 105, 105, 68, 24, 68, 67, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 136, 408, 105, 68, 68, 68, 24, 24, 5, 1] 603
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: 1317
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071117 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071117
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071117/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071117
Building REAL250005071118
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071118'
/scratch/stefan/7916153/working/building/REAL250005071118 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071118

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071118/0 /scratch/stefan/7916153/working/building/REAL250005071118 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 239)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/239
`/scratch/stefan/7916153/working/3D/239' -> `0.mol2'
Preparing input files

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

`REAL250005071118.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071118.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071118/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071118 none CCCCC(O)C(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 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: [200, 198, 188, 111, 82, 111, 82, 82, 50, 16, 50, 49, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 198, 198, 189, 189, 111, 333, 82, 50, 50, 50, 16, 16, 4, 1] 603
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: 1252
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071118 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071118
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071118/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071118
Building REAL250005071119
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071119'
/scratch/stefan/7916153/working/building/REAL250005071119 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071119

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071119/0 /scratch/stefan/7916153/working/building/REAL250005071119 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 240)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/240
`/scratch/stefan/7916153/working/3D/240' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CSC1CC1)

`REAL250005071119.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071119.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071119/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071119 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CSC1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 84, 122, 122, 175, 201, 201, 201, 201, 201, 201, 201, 201, 84, 27, 84, 6, 1, 1, 1, 1, 122, 122, 122, 175, 175, 201, 201, 84, 27, 27, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 815
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071119 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CSC1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 13, 29, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 29, 40, 40, 40, 110, 167, 201, 201, 29, 29, 29, 13, 13, 4, 1, 40, 110, 110, 201, 201, 201, 201, 201] 201
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: 669
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071119 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071119
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071119/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071119
Building REAL250005071120
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071120'
/scratch/stefan/7916153/working/building/REAL250005071120 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071120

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071120/0 /scratch/stefan/7916153/working/building/REAL250005071120 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 241)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/241
`/scratch/stefan/7916153/working/3D/241' -> `0.mol2'
Preparing input files

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

`REAL250005071120.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071120.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071120/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071120 none CCC(O)CC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.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', '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, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 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]
1  hydrogens need rotated
366  conformations in input
total number of sets (complete confs): 366
using faster count positions algorithm for large data
unique positions, atoms: [122, 121, 91, 121, 56, 56, 56, 33, 13, 33, 33, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 122, 121, 363, 91, 91, 56, 33, 33, 33, 13, 13, 4, 1] 366
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: 907
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071120 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071120
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071120/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071120
Building REAL250005071121
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071121'
/scratch/stefan/7916153/working/building/REAL250005071121 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071121

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071121/0 /scratch/stefan/7916153/working/building/REAL250005071121 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 242)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/242
`/scratch/stefan/7916153/working/3D/242' -> `0.mol2'
Preparing input files

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

`REAL250005071121.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071121.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071121/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071121 none CNC(=O)CCC(=O)N[C@H](C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', '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, 8, 1, 11, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 4, 7, 6, 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
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [199, 199, 159, 199, 141, 79, 79, 79, 54, 26, 54, 53, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 159, 159, 141, 141, 79, 54, 54, 54, 26, 26, 10, 1] 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])
total number of confs: 830
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071121 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071121
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071121/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071121
Building REAL250005071122
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071122'
/scratch/stefan/7916153/working/building/REAL250005071122 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071122

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071122/0 /scratch/stefan/7916153/working/building/REAL250005071122 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 243)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/243
`/scratch/stefan/7916153/working/3D/243' -> `0.mol2'
Preparing input files

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

`REAL250005071122.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071122.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071122/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071122 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CCCCF 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 13, 34, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 34, 48, 48, 48, 146, 180, 200, 200, 34, 34, 34, 13, 13, 4, 1, 48, 146, 146, 197, 197, 200, 200, 201, 201] 201
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, 36])
total number of confs: 981
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071122 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071122
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071122/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071122
Building REAL250005071123
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071123'
/scratch/stefan/7916153/working/building/REAL250005071123 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071123

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071123/0 /scratch/stefan/7916153/working/building/REAL250005071123 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 244)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/244
`/scratch/stefan/7916153/working/3D/244' -> `0.mol2'
Preparing input files

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

`REAL250005071123.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071123.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071123/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071123 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSN=C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 14, 8, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [21, 5, 21, 21, 75, 109, 109, 109, 115, 115, 115, 115, 115, 5, 1, 5, 1, 1, 1, 1, 1, 21, 21, 21, 75, 75, 109, 115, 5, 1, 1] 115
rigid atoms, others: [14, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 416
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071123 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CSN=C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 14, 8, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 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: [60, 21, 61, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 61, 88, 88, 88, 115, 115, 115, 115, 61, 61, 61, 21, 21, 9, 1, 88, 115, 115] 115
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])
total number of confs: 378
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071123 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071123
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071123/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071123
Building REAL250005071124
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071124'
/scratch/stefan/7916153/working/building/REAL250005071124 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071124

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071124/0 /scratch/stefan/7916153/working/building/REAL250005071124 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 245)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/245
`/scratch/stefan/7916153/working/3D/245' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(=O)C1)

`REAL250005071124.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071124.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071124/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071124 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(=O)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
185  conformations in input
total number of sets (complete confs): 185
using faster count positions algorithm for large data
unique positions, atoms: [40, 11, 40, 40, 122, 176, 176, 176, 185, 185, 185, 185, 185, 11, 1, 11, 1, 1, 1, 1, 1, 1, 40, 40, 40, 122, 122, 176, 185, 11, 1, 1, 1, 1, 1, 1, 1] 185
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 663
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071124 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC(=O)C1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
185  conformations in input
total number of sets (complete confs): 185
using faster count positions algorithm for large data
unique positions, atoms: [65, 27, 67, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 67, 115, 115, 115, 185, 185, 185, 185, 185, 67, 67, 67, 27, 27, 9, 1, 115, 185, 185, 185, 185, 185, 185, 185] 185
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])
total number of confs: 642
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071124 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071124
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071124/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071124
Building REAL250005071125
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071125'
/scratch/stefan/7916153/working/building/REAL250005071125 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071125

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071125/0 /scratch/stefan/7916153/working/building/REAL250005071125 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 246)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/246
`/scratch/stefan/7916153/working/3D/246' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CC(=O)N1)

`REAL250005071125.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071125.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071125/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071125 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 6, 4, 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: [30, 11, 30, 30, 60, 87, 87, 87, 90, 90, 90, 90, 90, 11, 1, 11, 1, 1, 1, 1, 1, 1, 30, 30, 30, 60, 60, 87, 90, 11, 1, 1, 1] 90
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 338
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071125 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)[C@H]1CC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 7, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 6, 4, 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: [50, 21, 52, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 52, 66, 66, 66, 90, 90, 90, 90, 90, 52, 52, 52, 20, 20, 7, 1, 66, 90, 90, 90] 90
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])
total number of confs: 330
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071125 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071125
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071125/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071125
Building REAL250005071126
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071126'
/scratch/stefan/7916153/working/building/REAL250005071126 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071126

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071126/0 /scratch/stefan/7916153/working/building/REAL250005071126 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 247)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/247
`/scratch/stefan/7916153/working/3D/247' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NC=N1)

`REAL250005071126.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071126.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071126/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071126 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NC=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [88, 47, 88, 88, 162, 197, 197, 197, 201, 201, 201, 201, 201, 47, 9, 47, 1, 1, 1, 1, 1, 1, 88, 88, 88, 162, 162, 197, 201, 47, 9, 9, 1, 1] 201
rigid atoms, others: [32, 33, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 796
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071126 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CN1C=NC=N1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [59, 24, 59, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 59, 88, 88, 88, 166, 201, 201, 201, 201, 59, 59, 59, 24, 24, 8, 1, 88, 166, 166, 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])
total number of confs: 726
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071126 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071126
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071126/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071126
Building REAL250005071127
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071127'
/scratch/stefan/7916153/working/building/REAL250005071127 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071127

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071127/0 /scratch/stefan/7916153/working/building/REAL250005071127 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 248)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/248
`/scratch/stefan/7916153/working/3D/248' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1(C(=O)N[C@H](C)CNC(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071127.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071127.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071127/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071127 none COC1(C(=O)N[C@H](C)CNC(=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', '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', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 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, 197, 126, 126, 126, 71, 27, 71, 69, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 197, 197, 201, 201, 201, 126, 71, 71, 71, 27, 27, 9, 1, 197, 197, 197, 197] 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: 711
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071127 none COC1(C(=O)N[C@H](C)CNC(=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', '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', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 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: [5, 1, 1, 1, 10, 10, 10, 41, 41, 41, 118, 184, 184, 184, 197, 197, 197, 197, 197, 1, 1, 5, 5, 5, 10, 41, 41, 41, 118, 118, 184, 197, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 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])
total number of confs: 690
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071127 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071127
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071127/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071127
Building REAL250005071128
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071128'
/scratch/stefan/7916153/working/building/REAL250005071128 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071128

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071128/0 /scratch/stefan/7916153/working/building/REAL250005071128 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 249)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/249
`/scratch/stefan/7916153/working/3D/249' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CSC1)

`REAL250005071128.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071128.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071128/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071128 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CSC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [40, 10, 40, 40, 105, 150, 150, 150, 161, 161, 161, 161, 161, 10, 1, 10, 1, 1, 1, 1, 40, 40, 40, 105, 105, 150, 161, 10, 1, 1, 1, 1, 1] 161
rigid atoms, others: [32, 14, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 573
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071128 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CSC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [74, 30, 75, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 75, 113, 113, 113, 161, 161, 161, 75, 75, 75, 30, 30, 10, 1, 113, 161, 161, 161, 161, 161] 161
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32])
total number of confs: 594
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071128 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071128
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071128/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071128
Building REAL250005071129
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071129'
/scratch/stefan/7916153/working/building/REAL250005071129 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071129

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071129/0 /scratch/stefan/7916153/working/building/REAL250005071129 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 250)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/250
`/scratch/stefan/7916153/working/3D/250' -> `0.mol2'
Preparing input files

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

`REAL250005071129.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071129.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071129/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071129 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=C(N)O1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [19, 5, 19, 19, 50, 85, 85, 85, 87, 87, 87, 87, 87, 5, 1, 5, 1, 1, 1, 1, 1, 1, 19, 19, 19, 50, 50, 85, 87, 5, 1, 2, 2] 87
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 318
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071129 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1=CN=C(N)O1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [51, 24, 51, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 51, 81, 81, 81, 87, 87, 87, 87, 87, 51, 51, 51, 24, 24, 8, 1, 81, 87, 87, 87] 87
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])
total number of confs: 306
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071129 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071129
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071129/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071129
Building REAL250005071130
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071130'
/scratch/stefan/7916153/working/building/REAL250005071130 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071130

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071130/0 /scratch/stefan/7916153/working/building/REAL250005071130 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 251)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/251
`/scratch/stefan/7916153/working/3D/251' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(CO)CC1)

`REAL250005071130.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071130.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071130/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071130 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(CO)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [64, 29, 64, 64, 115, 161, 161, 161, 162, 162, 162, 162, 162, 29, 6, 29, 1, 1, 1, 8, 1, 1, 64, 64, 64, 115, 115, 161, 162, 29, 6, 6, 8, 8, 24, 1, 1, 1, 1] 519
rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 696
number of broken/clashed sets: 53
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071130 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)CC1(CO)CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [31, 13, 31, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 31, 41, 41, 41, 128, 162, 173, 162, 162, 31, 31, 31, 13, 13, 4, 1, 41, 128, 128, 173, 173, 519, 162, 162, 162, 162] 519
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: 1226
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071130 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071130
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071130/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071130
Building REAL250005071131
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071131'
/scratch/stefan/7916153/working/building/REAL250005071131 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071131

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071131/0 /scratch/stefan/7916153/working/building/REAL250005071131 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 252)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/252
`/scratch/stefan/7916153/working/3D/252' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC=CO1)

`REAL250005071131.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071131.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071131/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071131 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC=CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [41, 12, 41, 41, 134, 184, 184, 184, 192, 192, 192, 192, 192, 12, 1, 12, 1, 1, 1, 1, 1, 1, 41, 41, 41, 134, 134, 184, 192, 12, 1, 1, 1, 1, 1, 1, 1] 192
rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21, 30, 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])
total number of confs: 702
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071131 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1CCC=CO1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [85, 39, 87, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 87, 136, 136, 136, 192, 192, 192, 192, 192, 87, 87, 87, 39, 39, 11, 1, 136, 192, 192, 192, 192, 192, 192, 192] 192
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])
total number of confs: 677
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071131 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071131
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071131/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071131
Building REAL250005071132
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071132'
/scratch/stefan/7916153/working/building/REAL250005071132 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071132

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071132/0 /scratch/stefan/7916153/working/building/REAL250005071132 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 253)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/253
`/scratch/stefan/7916153/working/3D/253' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CCCC1)

`REAL250005071132.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071132.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071132/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071132 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CCCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
432  conformations in input
total number of sets (complete confs): 432
using faster count positions algorithm for large data
unique positions, atoms: [31, 8, 31, 31, 90, 137, 137, 137, 144, 144, 144, 144, 144, 8, 1, 8, 1, 1, 1, 1, 1, 1, 31, 31, 31, 90, 90, 137, 144, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1] 432
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 521
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071132 none C[C@H](CNC(=O)C1=CC(=O)[N-]O1)NC(=O)C1(O)CCCC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
432  conformations in input
total number of sets (complete confs): 432
using faster count positions algorithm for large data
unique positions, atoms: [78, 33, 80, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 80, 120, 120, 120, 144, 144, 144, 144, 144, 80, 80, 80, 33, 33, 10, 1, 120, 432, 144, 144, 144, 144, 144, 144, 144, 144] 432
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: 959
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071132 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071132
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071132/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071132
Building REAL250005071133
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071133'
/scratch/stefan/7916153/working/building/REAL250005071133 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071133

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071133/0 /scratch/stefan/7916153/working/building/REAL250005071133 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 254)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/254
`/scratch/stefan/7916153/working/3D/254' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(C(=O)NC[C@@H](C)NC(=O)C2=CC(=O)[N-]O2)COC1)

`REAL250005071133.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071133.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071133/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071133 none CCC1(C(=O)NC[C@@H](C)NC(=O)C2=CC(=O)[N-]O2)COC1 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', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [145, 144, 97, 97, 97, 47, 19, 8, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 144, 144, 144, 145, 145, 145, 145, 145, 97, 47, 47, 19, 19, 19, 8, 1, 144, 144, 144, 144] 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: 486
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071133 none CCC1(C(=O)NC[C@@H](C)NC(=O)C2=CC(=O)[N-]O2)COC1 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', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 7, 7, 7, 33, 95, 94, 95, 137, 137, 137, 144, 144, 144, 144, 144, 1, 1, 1, 3, 3, 3, 3, 3, 7, 33, 33, 95, 95, 95, 137, 144, 1, 1, 1, 1] 145
rigid atoms, others: [1, 2, 3, 36, 37, 35, 19, 20, 21, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 563
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071133 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071133
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071133/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071133
Building REAL250005071134
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071134'
/scratch/stefan/7916153/working/building/REAL250005071134 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071134

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071134/0 /scratch/stefan/7916153/working/building/REAL250005071134 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 255)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/255
`/scratch/stefan/7916153/working/3D/255' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1(C)CCCO1)NC(=O)C1=CC(=O)[N-]O1)

`REAL250005071134.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071134.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071134/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071134 none C[C@H](CNC(=O)C1(C)CCCO1)NC(=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', 'O.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, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 7, 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
133  conformations in input
total number of sets (complete confs): 133
using faster count positions algorithm for large data
unique positions, atoms: [20, 8, 20, 20, 46, 94, 94, 94, 133, 133, 133, 133, 133, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 46, 46, 94, 133, 133, 133, 133, 133, 133, 133, 133, 133, 8, 1] 133
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: 453
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071134 none C[C@H](CNC(=O)C1(C)CCCO1)NC(=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', 'O.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, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 4, 7, 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
133  conformations in input
total number of sets (complete confs): 133
using faster count positions algorithm for large data
unique positions, atoms: [108, 57, 108, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 108, 128, 128, 128, 133, 133, 133, 133, 133, 108, 108, 108, 57, 57, 12, 2, 2, 2, 1, 1, 1, 1, 1, 1, 128, 133] 133
rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38])
total number of confs: 534
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071134 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071134
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071134/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071134
Building REAL250005071135
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071135'
/scratch/stefan/7916153/working/building/REAL250005071135 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071135

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071135/0 /scratch/stefan/7916153/working/building/REAL250005071135 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 256)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/256
`/scratch/stefan/7916153/working/3D/256' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1CC(=O)N1)NC(=O)C1=CC(=O)[N-]O1)

`REAL250005071135.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071135.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071135/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071135 none C[C@H](CNC(=O)C1CC(=O)N1)NC(=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.2', 'O.2', 'N.am', '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, 5, 8, 1, 11, 5, 5, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 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
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [20, 8, 20, 20, 42, 89, 89, 89, 134, 134, 134, 134, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 42, 42, 89, 134, 134, 134, 134, 8, 1] 134
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])
total number of confs: 462
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071135 none C[C@H](CNC(=O)C1CC(=O)N1)NC(=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.2', 'O.2', 'N.am', '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, 5, 8, 1, 11, 5, 5, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 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
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [117, 62, 117, 12, 12, 1, 12, 1, 1, 1, 1, 1, 117, 130, 130, 130, 134, 134, 134, 134, 134, 117, 117, 117, 62, 62, 12, 1, 1, 1, 1, 130, 134] 134
rigid atoms, others: [5, 7, 8, 9, 10, 11, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32])
total number of confs: 545
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071135 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071135
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071135/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071135
Building REAL250005071136
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071136'
/scratch/stefan/7916153/working/building/REAL250005071136 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071136

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071136/0 /scratch/stefan/7916153/working/building/REAL250005071136 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 257)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/257
`/scratch/stefan/7916153/working/3D/257' -> `0.mol2'
Preparing input files

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

`REAL250005071136.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071136.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071136/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071136 none C[C@H](CNC(=O)[C@H]1CCO[C@H]1C)NC(=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', 'H', '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', '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, 7, 5, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 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]
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: [21, 8, 21, 21, 52, 92, 92, 92, 106, 106, 106, 106, 106, 106, 106, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 52, 52, 92, 106, 106, 106, 106, 106, 106, 106, 8, 1] 106
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: 386
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071136 none C[C@H](CNC(=O)[C@H]1CCO[C@H]1C)NC(=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', 'H', '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', '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, 7, 5, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 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]
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: [72, 27, 73, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 73, 102, 102, 102, 106, 106, 106, 106, 106, 73, 73, 73, 27, 27, 5, 1, 1, 1, 1, 2, 2, 2, 102, 106] 106
rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 411
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071136 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071136
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071136/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071136
Building REAL250005071137
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071137'
/scratch/stefan/7916153/working/building/REAL250005071137 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071137

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071137/0 /scratch/stefan/7916153/working/building/REAL250005071137 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 258)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/258
`/scratch/stefan/7916153/working/3D/258' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1CC(F)C1)NC(=O)C1=CC(=O)[N-]O1)

`REAL250005071137.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071137.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071137/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071137 none C[C@H](CNC(=O)C1CC(F)C1)NC(=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', 'F', '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, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [23, 8, 23, 23, 65, 129, 129, 129, 201, 201, 201, 201, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 65, 65, 129, 201, 201, 201, 201, 201, 201, 8, 1] 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])
total number of confs: 673
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071137 none C[C@H](CNC(=O)C1CC(F)C1)NC(=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', 'F', '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, 5, 5, 15, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [140, 63, 141, 12, 12, 1, 12, 1, 1, 1, 1, 1, 141, 190, 191, 190, 201, 201, 201, 201, 201, 141, 141, 141, 63, 63, 12, 1, 1, 1, 1, 1, 1, 191, 201] 201
rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34])
total number of confs: 793
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071137 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071137
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071137/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071137
Building REAL250005071138
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071138'
/scratch/stefan/7916153/working/building/REAL250005071138 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071138

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071138/0 /scratch/stefan/7916153/working/building/REAL250005071138 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 259)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/259
`/scratch/stefan/7916153/working/3D/259' -> `0.mol2'
Preparing input files

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

`REAL250005071138.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071138.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071138/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071138 none CCC(O)C(C)C(=O)NC[C@@H](C)NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 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]
1  hydrogens need rotated
489  conformations in input
total number of sets (complete confs): 489
using faster count positions algorithm for large data
unique positions, atoms: [163, 146, 114, 147, 87, 114, 87, 87, 38, 16, 5, 16, 16, 5, 1, 5, 1, 1, 1, 1, 1, 1, 163, 163, 163, 162, 163, 147, 441, 114, 114, 114, 114, 87, 38, 38, 16, 16, 16, 5, 1] 489
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: 1143
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071138 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071138
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071138/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071138
Building REAL250005071139
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071139'
/scratch/stefan/7916153/working/building/REAL250005071139 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071139

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071139/0 /scratch/stefan/7916153/working/building/REAL250005071139 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 260)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/260
`/scratch/stefan/7916153/working/3D/260' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)CC1CC(=O)N1)NC(=O)C1=CC(=O)[N-]O1)

`REAL250005071139.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071139.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071139/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071139 none C[C@H](CNC(=O)CC1CC(=O)N1)NC(=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.2', 'O.2', 'N.am', '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, 5, 5, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 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: [12, 4, 12, 12, 35, 86, 86, 86, 184, 201, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 35, 35, 86, 184, 184, 201, 201, 201, 201, 5, 1] 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])
total number of confs: 782
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071139 none C[C@H](CNC(=O)CC1CC(=O)N1)NC(=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.2', 'O.2', 'N.am', '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, 5, 5, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 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: [183, 129, 183, 42, 42, 7, 42, 1, 1, 1, 1, 1, 1, 183, 200, 200, 200, 201, 201, 201, 201, 201, 183, 183, 183, 129, 129, 42, 7, 7, 1, 1, 1, 1, 200, 201] 201
rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 795
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071139 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071139
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071139/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071139
Building REAL250005071140
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071140'
/scratch/stefan/7916153/working/building/REAL250005071140 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071140

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071140/0 /scratch/stefan/7916153/working/building/REAL250005071140 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 261)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/261
`/scratch/stefan/7916153/working/3D/261' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C(O)C1CCC1)NC(=O)C1=CC(=O)[N-]O1)

`REAL250005071140.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071140.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071140/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071140 none C[C@H](CNC(=O)C(O)C1CCC1)NC(=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', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 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, 7, 7, 7]
1  hydrogens 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, 4, 12, 12, 36, 93, 93, 93, 172, 172, 201, 201, 201, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 36, 36, 93, 172, 516, 201, 201, 201, 201, 201, 201, 201, 4, 1] 603
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: 1322
number of broken/clashed sets: 76
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071140 none C[C@H](CNC(=O)C(O)C1CCC1)NC(=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', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 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, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [180, 120, 180, 35, 35, 7, 35, 1, 7, 1, 1, 1, 1, 180, 201, 201, 201, 201, 201, 201, 201, 201, 180, 180, 180, 120, 120, 35, 7, 21, 1, 1, 1, 1, 1, 1, 1, 201, 201] 603
rigid atoms, others: [32, 33, 34, 35, 36, 7, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38])
total number of confs: 835
number of broken/clashed sets: 76
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071140 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071140
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071140/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071140
Building REAL250005071141
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071141'
/scratch/stefan/7916153/working/building/REAL250005071141 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071141

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071141/0 /scratch/stefan/7916153/working/building/REAL250005071141 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 262)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/262
`/scratch/stefan/7916153/working/3D/262' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CNC(=O)C1=CC=NO1)NC(=O)C1=CC(=O)[N-]O1)

`REAL250005071141.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071141.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071141/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071141 none C[C@H](CNC(=O)C1=CC=NO1)NC(=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', 'C.2', 'C.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [16, 7, 16, 16, 42, 79, 79, 79, 91, 91, 91, 91, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 42, 42, 79, 91, 91, 7, 1] 91
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])
total number of confs: 307
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071141 none C[C@H](CNC(=O)C1=CC=NO1)NC(=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', 'C.2', 'C.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 8, 12, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [66, 34, 66, 8, 8, 1, 8, 1, 1, 1, 1, 1, 66, 88, 88, 88, 91, 91, 91, 91, 91, 66, 66, 66, 33, 33, 9, 1, 1, 88, 91] 91
rigid atoms, others: [5, 7, 8, 9, 10, 11, 27, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 351
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071141 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071141
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071141/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071141
Building REAL250005071142
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071142'
/scratch/stefan/7916153/working/building/REAL250005071142 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071142

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071142/0 /scratch/stefan/7916153/working/building/REAL250005071142 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 263)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/263
`/scratch/stefan/7916153/working/3D/263' -> `0.mol2'
Preparing input files

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

`REAL250005071142.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071142.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071142/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071142 none CCC(=O)NC[C@H]1CCCN(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', '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', '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, 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, 6, 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, 141, 141, 141, 85, 28, 28, 28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 201, 201, 201, 201, 201, 141, 85, 85, 28, 28, 28, 28, 28, 28, 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: 820
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071142 none CCC(=O)NC[C@H]1CCCN(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', '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', '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, 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, 6, 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: [110, 37, 37, 37, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 110, 110, 110, 110, 110, 37, 10, 10, 1, 1, 1, 1, 1, 1, 28, 1, 1] 201
rigid atoms, others: [32, 33, 34, 36, 5, 6, 7, 8, 9, 10, 11, 12, 37, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 35, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 437
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071142 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071142
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071142/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071142
Building REAL250005071143
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071143'
/scratch/stefan/7916153/working/building/REAL250005071143 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071143

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071143/0 /scratch/stefan/7916153/working/building/REAL250005071143 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 264)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/264
`/scratch/stefan/7916153/working/3D/264' -> `0.mol2'
Preparing input files

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

`REAL250005071143.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071143.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071143/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071143 none CC(=O)NC[C@H]1CCCN(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', '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', '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, 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, 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: [83, 83, 83, 68, 25, 25, 25, 25, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 83, 83, 83, 83, 68, 68, 25, 25, 25, 25, 25, 25, 1, 25, 25] 83
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: 278
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071143 none CC(=O)NC[C@H]1CCCN(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', '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', '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, 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, 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: [30, 30, 30, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 30, 30, 30, 30, 10, 10, 1, 1, 1, 1, 1, 1, 25, 1, 1] 83
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 32, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25])
total number of confs: 120
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071143 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071143
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071143/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071143
Building REAL250005071144
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071144'
/scratch/stefan/7916153/working/building/REAL250005071144 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071144

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071144/0 /scratch/stefan/7916153/working/building/REAL250005071144 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 265)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/265
`/scratch/stefan/7916153/working/3D/265' -> `0.mol2'
Preparing input files

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

`REAL250005071144.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071144.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071144/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071144 none O=C(NC[C@H]1CCCN(C(=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', '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: [11, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 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, 6, 7, 7, 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: [125, 125, 59, 21, 21, 21, 21, 21, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 125, 201, 201, 125, 59, 59, 21, 21, 21, 21, 21, 21, 1, 21, 21, 201, 201, 201, 201, 201] 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, 36, 37, 38])
total number of confs: 659
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071144 none O=C(NC[C@H]1CCCN(C(=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', '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: [11, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 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, 6, 7, 7, 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: [29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 29, 100, 100, 29, 8, 8, 1, 1, 1, 1, 1, 1, 20, 1, 1, 100, 100, 100, 100, 100] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 18, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 31, 34, 35, 36, 37, 38])
total number of confs: 298
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071144 none O=C(NC[C@H]1CCCN(C(=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', '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: [11, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 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, 6, 7, 7, 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, 48, 100, 100, 100, 100, 100, 100, 190, 190, 201, 201, 201, 201, 201, 100, 1, 1, 1, 11, 48, 48, 100, 100, 100, 100, 100, 100, 201, 100, 100, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 34, 35, 36, 37, 38, 19, 20, 21] 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, 31, 32, 33])
total number of confs: 611
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071144 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071144
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071144/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071144
Building REAL250005071145
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071145'
/scratch/stefan/7916153/working/building/REAL250005071145 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071145

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071145/0 /scratch/stefan/7916153/working/building/REAL250005071145 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 266)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/266
`/scratch/stefan/7916153/working/3D/266' -> `0.mol2'
Preparing input files

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

`REAL250005071145.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071145.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071145/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071145 none COCC(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 7, 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]
dock color type numbers: [7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 157, 157, 157, 62, 18, 18, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 201, 201, 201, 201, 201, 157, 62, 62, 18, 18, 18, 18, 18, 18, 1, 18, 18] 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: 740
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071145 none COCC(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 7, 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]
dock color type numbers: [7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [111, 93, 32, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 1, 111, 111, 111, 93, 93, 32, 8, 8, 1, 1, 1, 1, 1, 1, 18, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 37, 6, 7, 8, 9, 10, 11, 12, 13, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 410
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071145 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071145
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071145/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071145
Building REAL250005071146
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071146'
/scratch/stefan/7916153/working/building/REAL250005071146 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071146

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071146/0 /scratch/stefan/7916153/working/building/REAL250005071146 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 267)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/267
`/scratch/stefan/7916153/working/3D/267' -> `0.mol2'
Preparing input files

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

`REAL250005071146.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071146.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071146/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071146 none CCCC(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 5, 1, 11, 8, 5, 5, 7, 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, 7]
dock color type numbers: [7, 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]
0  hydrogens need 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, 114, 114, 114, 49, 17, 17, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 201, 201, 201, 201, 201, 195, 195, 114, 49, 49, 17, 17, 17, 17, 17, 17, 1, 17, 17] 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, 39, 40])
total number of confs: 810
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071146 none CCCC(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 5, 1, 11, 8, 5, 5, 7, 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, 7]
dock color type numbers: [7, 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]
0  hydrogens 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, 99, 24, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 1, 121, 121, 121, 121, 121, 99, 99, 24, 6, 6, 1, 1, 1, 1, 1, 1, 17, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 21, 39] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38])
total number of confs: 554
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071146 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071146
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071146/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071146
Building REAL250005071147
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071147'
/scratch/stefan/7916153/working/building/REAL250005071147 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071147

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071147/0 /scratch/stefan/7916153/working/building/REAL250005071147 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 268)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/268
`/scratch/stefan/7916153/working/3D/268' -> `0.mol2'
Preparing input files

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

`REAL250005071147.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071147.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071147/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071147 none CC(C)C(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 5, 1, 11, 8, 5, 5, 7, 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, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 166, 201, 166, 166, 75, 23, 23, 23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 201, 201, 201, 201, 201, 201, 201, 166, 75, 75, 23, 23, 23, 23, 23, 23, 1, 23, 23] 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, 39, 40])
total number of confs: 734
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071147 none CC(C)C(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 5, 1, 11, 8, 5, 5, 7, 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, 7]
dock color type numbers: [7, 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]
0  hydrogens 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, 36, 95, 36, 36, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 95, 95, 95, 95, 95, 95, 95, 36, 9, 9, 1, 1, 1, 1, 1, 1, 23, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 40, 21, 39] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38])
total number of confs: 391
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071147 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071147
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071147/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071147
Building REAL250005071148
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071148'
/scratch/stefan/7916153/working/building/REAL250005071148 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071148

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071148/0 /scratch/stefan/7916153/working/building/REAL250005071148 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 269)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/269
`/scratch/stefan/7916153/working/3D/269' -> `0.mol2'
Preparing input files

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

`REAL250005071148.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071148.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071148/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071148 none NC(=O)C(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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: [8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 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, 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: [200, 200, 201, 200, 200, 139, 42, 42, 42, 42, 42, 42, 12, 1, 12, 1, 1, 1, 1, 1, 1, 42, 200, 201, 200, 139, 139, 42, 42, 42, 42, 42, 42, 1, 42, 42] 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: 674
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071148 none NC(=O)C(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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: [8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 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, 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, 46, 68, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 42, 42, 42, 42, 42, 1, 67, 68, 46, 10, 10, 1, 1, 1, 1, 1, 1, 42, 1, 1] 201
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 33, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26])
total number of confs: 255
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071148 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071148
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071148/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071148
Building REAL250005071149
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071149'
/scratch/stefan/7916153/working/building/REAL250005071149 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071149

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071149/0 /scratch/stefan/7916153/working/building/REAL250005071149 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 270)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/270
`/scratch/stefan/7916153/working/3D/270' -> `0.mol2'
Preparing input files

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

`REAL250005071149.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071149.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071149/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071149 none C=CCC(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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: [1, 1, 5, 1, 11, 8, 5, 5, 7, 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]
dock color type numbers: [7, 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]
0  hydrogens 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, 135, 135, 135, 63, 22, 22, 22, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 201, 201, 201, 201, 201, 135, 63, 63, 22, 22, 22, 22, 22, 22, 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: 788
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071149 none C=CCC(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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: [1, 1, 5, 1, 11, 8, 5, 5, 7, 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]
dock color type numbers: [7, 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]
0  hydrogens 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, 109, 27, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 143, 143, 143, 109, 109, 27, 6, 6, 1, 1, 1, 1, 1, 1, 22, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 37, 6, 7, 8, 9, 10, 11, 12, 13, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 556
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071149 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071149
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071149/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071149
Building REAL250005071150
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071150'
/scratch/stefan/7916153/working/building/REAL250005071150 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071150

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071150/0 /scratch/stefan/7916153/working/building/REAL250005071150 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 271)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/271
`/scratch/stefan/7916153/working/3D/271' -> `0.mol2'
Preparing input files

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

`REAL250005071150.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071150.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071150/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071150 none O=C(CO)NC[C@H]1CCCN(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', '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', '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, 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, 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: [198, 198, 198, 201, 125, 36, 36, 36, 36, 36, 36, 11, 1, 11, 1, 1, 1, 1, 1, 1, 36, 201, 201, 603, 198, 125, 125, 36, 36, 36, 36, 36, 36, 1, 36, 36] 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: 1298
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071150 none O=C(CO)NC[C@H]1CCCN(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', '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', '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, 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, 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: [41, 41, 41, 92, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 93, 93, 279, 41, 10, 10, 1, 1, 1, 1, 1, 1, 36, 1, 1] 603
rigid atoms, others: [32, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 33, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26])
total number of confs: 676
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071150 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071150
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071150/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071150
Building REAL250005071151
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071151'
/scratch/stefan/7916153/working/building/REAL250005071151 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071151

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071151/0 /scratch/stefan/7916153/working/building/REAL250005071151 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 272)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/272
`/scratch/stefan/7916153/working/3D/272' -> `0.mol2'
Preparing input files

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

`REAL250005071151.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071151.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071151/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071151 none CC(O)C(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 5, 5, 7, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 197, 201, 197, 197, 111, 31, 31, 31, 31, 31, 31, 10, 1, 10, 1, 1, 1, 1, 1, 1, 31, 201, 201, 201, 201, 603, 197, 111, 111, 31, 31, 31, 31, 31, 31, 1, 31, 31] 603
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: 1269
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071151 none CC(O)C(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 5, 5, 7, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [97, 39, 94, 39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 97, 97, 97, 97, 291, 39, 10, 10, 1, 1, 1, 1, 1, 1, 31, 1, 1] 603
rigid atoms, others: [32, 33, 34, 35, 37, 6, 7, 8, 9, 10, 11, 12, 13, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 697
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071151 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071151
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071151/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071151
Building REAL250005071152
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071152'
/scratch/stefan/7916153/working/building/REAL250005071152 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071152

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071152/0 /scratch/stefan/7916153/working/building/REAL250005071152 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 273)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/273
`/scratch/stefan/7916153/working/3D/273' -> `0.mol2'
Preparing input files

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

`REAL250005071152.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071152.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071152/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071152 none O=C(CCF)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 15, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 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
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, 49, 16, 16, 16, 16, 16, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 201, 201, 201, 201, 119, 49, 49, 16, 16, 16, 16, 16, 16, 1, 16, 16] 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: 765
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071152 none O=C(CCF)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 15, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 106, 126, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1, 106, 106, 126, 126, 24, 6, 6, 1, 1, 1, 1, 1, 1, 16, 1, 1] 201
rigid atoms, others: [32, 33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 510
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071152 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071152
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071152/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071152
Building REAL250005071153
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071153'
/scratch/stefan/7916153/working/building/REAL250005071153 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071153

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071153/0 /scratch/stefan/7916153/working/building/REAL250005071153 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 274)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/274
`/scratch/stefan/7916153/working/3D/274' -> `0.mol2'
Preparing input files

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

`REAL250005071153.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071153.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071153/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071153 none C[C@@H](O)C(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 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, 7, 7, 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, 192, 201, 199, 192, 192, 105, 30, 30, 30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 201, 201, 201, 603, 192, 105, 105, 30, 30, 30, 30, 30, 30, 1, 30, 30] 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: 1276
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071153 none C[C@@H](O)C(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 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, 7, 7, 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: [107, 45, 107, 102, 45, 45, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 107, 107, 107, 321, 45, 10, 10, 1, 1, 1, 1, 1, 1, 30, 1, 1] 603
rigid atoms, others: [32, 33, 34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 755
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071153 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071153
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071153/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071153
Building REAL250005071154
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071154'
/scratch/stefan/7916153/working/building/REAL250005071154 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071154

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071154/0 /scratch/stefan/7916153/working/building/REAL250005071154 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 275)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/275
`/scratch/stefan/7916153/working/3D/275' -> `0.mol2'
Preparing input files

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

`REAL250005071154.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071154.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071154/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071154 none C[C@H](O)C(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 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, 7, 7, 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, 197, 201, 201, 197, 197, 111, 31, 31, 31, 31, 31, 31, 10, 1, 10, 1, 1, 1, 1, 1, 1, 31, 201, 201, 201, 603, 197, 111, 111, 31, 31, 31, 31, 31, 31, 1, 31, 31] 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: 1269
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071154 none C[C@H](O)C(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 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, 7, 7, 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: [97, 39, 97, 94, 39, 39, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 97, 97, 97, 291, 39, 10, 10, 1, 1, 1, 1, 1, 1, 31, 1, 1] 603
rigid atoms, others: [32, 33, 34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 697
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071154 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071154
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071154/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071154
Building REAL250005071155
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071155'
/scratch/stefan/7916153/working/building/REAL250005071155 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071155

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071155/0 /scratch/stefan/7916153/working/building/REAL250005071155 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 276)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/276
`/scratch/stefan/7916153/working/3D/276' -> `0.mol2'
Preparing input files

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

`REAL250005071155.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071155.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071155/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071155 none CC=CC(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 11, 8, 5, 5, 7, 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]
dock color type numbers: [7, 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]
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, 159, 159, 159, 86, 26, 26, 26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 198, 198, 198, 198, 198, 159, 86, 86, 26, 26, 26, 26, 26, 26, 1, 26, 26] 198
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: 666
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071155 none CC=CC(=O)NC[C@H]1CCCN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 11, 8, 5, 5, 7, 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]
dock color type numbers: [7, 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]
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: [98, 98, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 98, 98, 98, 98, 98, 37, 9, 9, 1, 1, 1, 1, 1, 1, 26, 1, 1] 198
rigid atoms, others: [32, 33, 34, 35, 37, 6, 7, 8, 9, 10, 11, 12, 13, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 317
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071155 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071155
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071155/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071155
Building REAL250005071156
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071156'
/scratch/stefan/7916153/working/building/REAL250005071156 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071156

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071156/0 /scratch/stefan/7916153/working/building/REAL250005071156 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 277)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/277
`/scratch/stefan/7916153/working/3D/277' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N1CCC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071156.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071156.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071156/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071156 none COCC(=O)N1CCC[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', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 7, 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, 3, 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]
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, 165, 102, 62, 102, 62, 62, 62, 58, 23, 62, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 62, 176, 176, 176, 165, 165, 62, 62, 62, 62, 62, 62, 23, 23, 6, 1, 62, 62] 176
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: 674
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071156 none COCC(=O)N1CCC[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', '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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 7, 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, 3, 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]
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: [59, 25, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 9, 44, 44, 44, 62, 62, 62, 62, 62, 1, 59, 59, 59, 25, 25, 1, 1, 1, 1, 1, 1, 9, 9, 44, 62, 1, 1] 176
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 38, 37, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 33, 34, 35, 36])
total number of confs: 278
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071156 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071156
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071156/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071156
Building REAL250005071157
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071157'
/scratch/stefan/7916153/working/building/REAL250005071157 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071157

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071157/0 /scratch/stefan/7916153/working/building/REAL250005071157 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 278)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/278
`/scratch/stefan/7916153/working/3D/278' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N1CCC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071157.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071157.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071157/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071157 none CCCC(=O)N1CCC[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', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 195, 149, 68, 149, 68, 68, 68, 63, 20, 68, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 68, 201, 201, 201, 201, 201, 195, 195, 68, 68, 68, 68, 68, 68, 20, 20, 6, 1, 68, 68] 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, 39, 40])
total number of confs: 747
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071157 none CCCC(=O)N1CCC[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', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 51, 51, 51, 68, 68, 68, 68, 68, 1, 33, 33, 33, 32, 32, 19, 19, 1, 1, 1, 1, 1, 1, 10, 10, 51, 68, 1, 1] 201
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 40, 21, 39, 29, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38])
total number of confs: 321
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071157 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071157
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071157/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071157
Building REAL250005071158
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071158'
/scratch/stefan/7916153/working/building/REAL250005071158 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071158

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071158/0 /scratch/stefan/7916153/working/building/REAL250005071158 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 279)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/279
`/scratch/stefan/7916153/working/3D/279' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N1CCC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071158.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071158.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071158/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071158 none CC(C)C(=O)N1CCC[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', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [143, 143, 143, 77, 143, 77, 77, 77, 74, 29, 77, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 77, 143, 143, 143, 143, 143, 143, 143, 77, 77, 77, 77, 77, 77, 29, 29, 7, 1, 77, 77] 143
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: 432
number of broken/clashed sets: 90
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071158 none CC(C)C(=O)N1CCC[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', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 1, 10, 54, 54, 54, 77, 77, 77, 77, 77, 1, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 10, 10, 54, 77, 1, 1] 143
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 40, 21, 39, 29, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38])
total number of confs: 249
number of broken/clashed sets: 90
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071158 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071158
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071158/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071158
Building REAL250005071159
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071159'
/scratch/stefan/7916153/working/building/REAL250005071159 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071159

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071159/0 /scratch/stefan/7916153/working/building/REAL250005071159 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 280)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/280
`/scratch/stefan/7916153/working/3D/280' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1CCC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071159.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071159.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071159/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071159 none CCC(=O)N1CCC[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', '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, 7, 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, 4, 7, 6, 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
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [127, 125, 73, 125, 73, 73, 73, 70, 26, 73, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 73, 127, 127, 127, 127, 127, 73, 73, 73, 73, 73, 73, 26, 26, 6, 1, 73, 73] 127
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: 406
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071159 none CCC(=O)N1CCC[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', '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, 7, 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, 4, 7, 6, 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
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 52, 52, 52, 73, 73, 73, 73, 73, 1, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 10, 10, 52, 73, 1, 1] 127
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 37, 20, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 3, 33, 35, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25])
total number of confs: 243
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071159 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071159
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071159/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071159
Building REAL250005071160
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071160'
/scratch/stefan/7916153/working/building/REAL250005071160 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071160

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071160/0 /scratch/stefan/7916153/working/building/REAL250005071160 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 281)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/281
`/scratch/stefan/7916153/working/3D/281' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071160.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071160.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071160/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071160 none CC(=O)N1CCC[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', '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, 7, 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, 4, 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
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [81, 70, 81, 70, 70, 70, 70, 33, 70, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 70, 81, 81, 81, 70, 70, 70, 70, 70, 70, 33, 33, 8, 1, 70, 70] 81
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: 254
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071160 none CC(=O)N1CCC[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', '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, 7, 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, 4, 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
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 10, 49, 49, 49, 70, 70, 70, 70, 70, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 10, 10, 49, 70, 1, 1] 81
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 33, 19, 23, 24, 25, 26, 27, 28] set([0, 32, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 29, 30, 31])
total number of confs: 175
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071160 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071160
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071160/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071160
Building REAL250005071161
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071161'
/scratch/stefan/7916153/working/building/REAL250005071161 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071161

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071161/0 /scratch/stefan/7916153/working/building/REAL250005071161 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 282)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/282
`/scratch/stefan/7916153/working/3D/282' -> `0.mol2'
Preparing input files

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

`REAL250005071161.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071161.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071161/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071161 none O=C(NC[C@H]1CCCN(C(=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', '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', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 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, 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, 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: [139, 139, 79, 20, 20, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 20, 139, 143, 143, 143, 143, 143, 139, 79, 79, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 20, 20, 143] 143
rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 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, 28, 29, 30, 36, 37, 38])
total number of confs: 467
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071161 none O=C(NC[C@H]1CCCN(C(=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', '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', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 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, 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, 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: [53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 1, 53, 79, 79, 79, 79, 79, 53, 10, 10, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 1, 1, 79] 143
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 15, 37, 25, 26, 27, 28, 29, 30, 36] set([0, 1, 2, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 38])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071161 none O=C(NC[C@H]1CCCN(C(=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', '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', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 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, 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, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 26, 79, 79, 79, 79, 79, 79, 111, 111, 143, 143, 79, 1, 1, 1, 1, 1, 1, 7, 26, 26, 79, 79, 79, 79, 79, 79, 143, 143, 143, 143, 143, 79, 79, 1] 143
rigid atoms, others: [1, 38, 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, 35, 36, 37])
total number of confs: 471
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071161 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071161
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071161/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071161
Building REAL250005071162
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071162'
/scratch/stefan/7916153/working/building/REAL250005071162 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071162

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071162/0 /scratch/stefan/7916153/working/building/REAL250005071162 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 283)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/283
`/scratch/stefan/7916153/working/3D/283' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C(=O)N1CCC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071162.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071162.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071162/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071162 none NC(=O)C(=O)N1CCC[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', '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: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 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
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 20, 25, 19, 20, 19, 19, 19, 19, 13, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 19, 25, 25, 19, 19, 19, 19, 19, 19, 13, 13, 5, 1, 19, 19] 25
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: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071162 none NC(=O)C(=O)N1CCC[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', '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: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 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
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [11, 4, 11, 1, 4, 1, 1, 1, 1, 1, 1, 1, 6, 18, 18, 18, 19, 19, 19, 19, 19, 1, 11, 11, 1, 1, 1, 1, 1, 1, 6, 6, 18, 19, 1, 1] 25
rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 35, 21, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 4, 33, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 30, 31])
total number of confs: 77
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071162 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071162
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071162/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071162
Building REAL250005071163
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071163'
/scratch/stefan/7916153/working/building/REAL250005071163 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071163

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071163/0 /scratch/stefan/7916153/working/building/REAL250005071163 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 284)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/284
`/scratch/stefan/7916153/working/3D/284' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N1CCC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071163.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071163.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071163/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071163 none O=C(CO)N1CCC[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', '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, 7, 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, 4, 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
243  conformations in input
total number of sets (complete confs): 243
using faster count positions algorithm for large data
unique positions, atoms: [76, 52, 76, 81, 52, 52, 52, 49, 21, 52, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 52, 81, 81, 243, 52, 52, 52, 52, 52, 52, 21, 21, 8, 1, 52, 52] 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])
total number of confs: 529
number of broken/clashed sets: 46
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071163 none O=C(CO)N1CCC[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', '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, 7, 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, 4, 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
243  conformations in input
total number of sets (complete confs): 243
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 15, 1, 1, 1, 1, 1, 1, 1, 10, 40, 40, 40, 52, 52, 52, 52, 52, 1, 15, 15, 45, 1, 1, 1, 1, 1, 1, 10, 10, 40, 52, 1, 1] 243
rigid atoms, others: [1, 34, 35, 4, 5, 6, 7, 8, 9, 10, 20, 24, 25, 26, 27, 28, 29] set([0, 32, 2, 3, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 30, 31])
total number of confs: 221
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071163 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071163
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071163/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071163
Building REAL250005071164
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071164'
/scratch/stefan/7916153/working/building/REAL250005071164 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071164

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071164/0 /scratch/stefan/7916153/working/building/REAL250005071164 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 285)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/285
`/scratch/stefan/7916153/working/3D/285' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N1CCC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071164.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071164.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071164/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071164 none CC(O)C(=O)N1CCC[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', '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, 12, 1, 11, 8, 5, 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, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 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]
1  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [62, 56, 62, 38, 56, 38, 38, 38, 37, 16, 38, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 38, 62, 62, 62, 62, 186, 38, 38, 38, 38, 38, 38, 16, 16, 7, 1, 38, 38] 186
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: 396
number of broken/clashed sets: 87
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071164 none CC(O)C(=O)N1CCC[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', '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, 12, 1, 11, 8, 5, 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, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 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]
1  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 1, 9, 34, 34, 34, 38, 38, 38, 38, 38, 1, 15, 15, 15, 15, 45, 1, 1, 1, 1, 1, 1, 9, 9, 34, 38, 1, 1] 186
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 38, 37, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 33, 34, 35, 36])
total number of confs: 195
number of broken/clashed sets: 87
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071164 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071164
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071164/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071164
Building REAL250005071165
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071165'
/scratch/stefan/7916153/working/building/REAL250005071165 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071165

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071165/0 /scratch/stefan/7916153/working/building/REAL250005071165 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 286)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/286
`/scratch/stefan/7916153/working/3D/286' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C(=O)N1CCC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071165.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071165.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071165/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071165 none CC(=O)C(=O)N1CCC[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', '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, 1, 11, 8, 5, 5, 5, 5, 7, 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, 3, 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
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [37, 33, 37, 30, 33, 30, 30, 30, 30, 16, 30, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 30, 37, 37, 37, 30, 30, 30, 30, 30, 30, 16, 16, 6, 1, 30, 30] 37
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: 125
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071165 none CC(=O)C(=O)N1CCC[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', '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, 1, 11, 8, 5, 5, 5, 5, 7, 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, 3, 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
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [11, 4, 11, 1, 4, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 30, 30, 30, 30, 30, 1, 11, 11, 11, 1, 1, 1, 1, 1, 1, 9, 9, 23, 30, 1, 1] 37
rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 11, 35, 21, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 34, 4, 33, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 31])
total number of confs: 107
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071165 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071165
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071165/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071165
Building REAL250005071166
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071166'
/scratch/stefan/7916153/working/building/REAL250005071166 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071166

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071166/0 /scratch/stefan/7916153/working/building/REAL250005071166 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 287)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/287
`/scratch/stefan/7916153/working/3D/287' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N1CCC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071166.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071166.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071166/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071166 none CC=CC(=O)N1CCC[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', '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, 1, 1, 11, 8, 5, 5, 5, 5, 7, 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, 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]
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, 130, 80, 130, 80, 80, 80, 74, 25, 80, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 80, 146, 146, 146, 146, 146, 80, 80, 80, 80, 80, 80, 25, 25, 4, 1, 80, 80] 146
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: 491
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071166 none CC=CC(=O)N1CCC[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', '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, 1, 1, 11, 8, 5, 5, 5, 5, 7, 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, 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]
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: [32, 32, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 10, 55, 55, 55, 80, 80, 80, 80, 80, 1, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 10, 10, 55, 80, 1, 1] 146
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 38, 37, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 33, 34, 35, 36])
total number of confs: 264
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071166 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071166
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071166/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071166
Building REAL250005071167
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071167'
/scratch/stefan/7916153/working/building/REAL250005071167 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071167

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071167/0 /scratch/stefan/7916153/working/building/REAL250005071167 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 288)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/288
`/scratch/stefan/7916153/working/3D/288' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N1CCC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071167.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071167.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071167/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071167 none C[C@H](O)C(=O)N1CCC[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', '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, 7, 12, 1, 11, 8, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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]
1  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [62, 56, 62, 62, 38, 56, 38, 38, 38, 38, 16, 38, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 38, 62, 62, 62, 186, 38, 38, 38, 38, 38, 38, 16, 16, 7, 1, 38, 38] 186
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: 391
number of broken/clashed sets: 87
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071167 none C[C@H](O)C(=O)N1CCC[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', '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, 7, 12, 1, 11, 8, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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]
1  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [15, 6, 15, 15, 1, 6, 1, 1, 1, 1, 1, 1, 1, 9, 34, 34, 34, 38, 38, 38, 38, 38, 1, 15, 15, 15, 45, 1, 1, 1, 1, 1, 1, 9, 9, 34, 38, 1, 1] 186
rigid atoms, others: [32, 4, 37, 6, 7, 8, 9, 10, 11, 12, 38, 22, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 33, 34, 35, 36])
total number of confs: 195
number of broken/clashed sets: 87
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071167 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071167
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071167/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071167
Building REAL250005071168
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071168'
/scratch/stefan/7916153/working/building/REAL250005071168 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071168

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071168/0 /scratch/stefan/7916153/working/building/REAL250005071168 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 289)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/289
`/scratch/stefan/7916153/working/3D/289' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N1CCC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071168.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071168.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071168/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071168 none C=CCC(=O)N1CCC[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', '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: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 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, 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]
0  hydrogens need rotated
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, 72, 144, 72, 72, 72, 68, 24, 72, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 72, 72, 72, 72, 72, 72, 24, 24, 6, 1, 72, 72] 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: 754
number of broken/clashed sets: 59
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071168 none C=CCC(=O)N1CCC[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', '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: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [62, 26, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 54, 54, 54, 72, 72, 72, 72, 72, 1, 62, 62, 62, 26, 26, 1, 1, 1, 1, 1, 1, 10, 10, 54, 72, 1, 1] 201
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 38, 37, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 33, 34, 35, 36])
total number of confs: 365
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071168 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071168
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071168/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071168
Building REAL250005071169
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071169'
/scratch/stefan/7916153/working/building/REAL250005071169 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071169

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071169/0 /scratch/stefan/7916153/working/building/REAL250005071169 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 290)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/290
`/scratch/stefan/7916153/working/3D/290' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CCC(=O)N1CCC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071169.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071169.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071169/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071169 none N#CCC(=O)N1CCC[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', '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: [8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 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
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [139, 139, 106, 52, 106, 52, 52, 52, 48, 18, 52, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 52, 139, 139, 52, 52, 52, 52, 52, 52, 18, 18, 6, 1, 52, 52] 139
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: 520
number of broken/clashed sets: 39
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071169 none N#CCC(=O)N1CCC[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', '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: [8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 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
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 45, 45, 45, 52, 52, 52, 52, 52, 1, 27, 27, 1, 1, 1, 1, 1, 1, 10, 10, 45, 52, 1, 1] 139
rigid atoms, others: [34, 3, 5, 6, 7, 8, 9, 10, 11, 35, 21, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 4, 33, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 30, 31])
total number of confs: 225
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071169 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071169
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071169/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071169
Building REAL250005071170
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071170'
/scratch/stefan/7916153/working/building/REAL250005071170 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071170

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071170/0 /scratch/stefan/7916153/working/building/REAL250005071170 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 291)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/291
`/scratch/stefan/7916153/working/3D/291' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)N1CCC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071170.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071170.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071170/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071170 none O=C(CCF)N1CCC[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', '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: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 7, 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: [6, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [148, 66, 148, 201, 201, 66, 66, 66, 61, 21, 66, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 66, 66, 66, 66, 66, 66, 21, 21, 5, 1, 66, 66] 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: 732
number of broken/clashed sets: 56
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071170 none O=C(CCF)N1CCC[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', '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: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 7, 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: [6, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 24, 41, 1, 1, 1, 1, 1, 1, 1, 10, 51, 51, 51, 66, 66, 66, 66, 66, 1, 24, 24, 41, 41, 1, 1, 1, 1, 1, 1, 10, 10, 51, 66, 1, 1] 201
rigid atoms, others: [1, 36, 5, 6, 7, 8, 9, 10, 11, 37, 21, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 35, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 34])
total number of confs: 334
number of broken/clashed sets: 56
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071170 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071170
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071170/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071170
Building REAL250005071171
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071171'
/scratch/stefan/7916153/working/building/REAL250005071171 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071171

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071171/0 /scratch/stefan/7916153/working/building/REAL250005071171 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 292)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/292
`/scratch/stefan/7916153/working/3D/292' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N1CCC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071171.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071171.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071171/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071171 none C[C@@H](O)C(=O)N1CCC[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', '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, 7, 12, 1, 11, 8, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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]
1  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [53, 48, 53, 53, 35, 48, 35, 35, 35, 35, 15, 35, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 35, 53, 53, 53, 159, 35, 35, 35, 35, 35, 35, 15, 15, 5, 1, 35, 35] 159
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: 338
number of broken/clashed sets: 81
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071171 none C[C@@H](O)C(=O)N1CCC[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', '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, 7, 12, 1, 11, 8, 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, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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]
1  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [10, 4, 10, 10, 1, 4, 1, 1, 1, 1, 1, 1, 1, 9, 32, 32, 32, 35, 35, 35, 35, 35, 1, 10, 10, 10, 30, 1, 1, 1, 1, 1, 1, 9, 9, 32, 35, 1, 1] 159
rigid atoms, others: [32, 4, 37, 6, 7, 8, 9, 10, 11, 12, 38, 22, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 33, 34, 35, 36])
total number of confs: 162
number of broken/clashed sets: 81
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071171 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071171
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071171/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071171
Building REAL250005071172
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071172'
/scratch/stefan/7916153/working/building/REAL250005071172 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071172

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071172/0 /scratch/stefan/7916153/working/building/REAL250005071172 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 293)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/293
`/scratch/stefan/7916153/working/3D/293' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N1CCC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071172.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071172.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071172/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071172 none C=CC(=O)N1CCC[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', '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: [1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 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, 4, 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
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [103, 103, 65, 103, 65, 65, 65, 62, 23, 65, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 65, 103, 103, 103, 65, 65, 65, 65, 65, 65, 23, 23, 6, 1, 65, 65] 103
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: 332
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071172 none C=CC(=O)N1CCC[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', '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: [1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 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, 4, 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
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [27, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 10, 52, 52, 52, 65, 65, 65, 65, 65, 1, 27, 27, 27, 1, 1, 1, 1, 1, 1, 10, 10, 52, 65, 1, 1] 103
rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 34, 20, 24, 25, 26, 27, 28, 29] set([0, 1, 3, 33, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 30, 31])
total number of confs: 225
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071172 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071172
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071172/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071172
Building REAL250005071173
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071173'
/scratch/stefan/7916153/working/building/REAL250005071173 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071173

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071173/0 /scratch/stefan/7916153/working/building/REAL250005071173 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 294)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/294
`/scratch/stefan/7916153/working/3D/294' -> `0.mol2'
Preparing input files

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

`REAL250005071173.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071173.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071173/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071173 none CCC(=O)N1CC(N(C)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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
179  conformations in input
total number of sets (complete confs): 179
using faster count positions algorithm for large data
unique positions, atoms: [179, 129, 93, 129, 93, 93, 33, 11, 33, 1, 11, 1, 1, 1, 1, 1, 1, 93, 179, 179, 179, 179, 179, 93, 93, 93, 33, 33, 33, 1, 93, 93] 179
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: 687
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071173 none CCC(=O)N1CC(N(C)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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
179  conformations in input
total number of sets (complete confs): 179
using faster count positions algorithm for large data
unique positions, atoms: [19, 6, 1, 6, 1, 1, 1, 1, 11, 11, 42, 42, 93, 93, 93, 93, 93, 1, 19, 19, 19, 19, 19, 1, 1, 1, 11, 11, 11, 93, 1, 1] 179
rigid atoms, others: [2, 4, 5, 6, 7, 17, 23, 24, 25, 30, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 26, 27, 28, 29])
total number of confs: 242
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071173 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071173
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071173/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071173
Building REAL250005071174
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071174'
/scratch/stefan/7916153/working/building/REAL250005071174 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071174

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071174/0 /scratch/stefan/7916153/working/building/REAL250005071174 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 295)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/295
`/scratch/stefan/7916153/working/3D/295' -> `0.mol2'
Preparing input files

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

`REAL250005071174.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071174.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071174/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071174 none COCCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 180, 80, 52, 80, 52, 52, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 52, 201, 201, 201, 201, 201, 180, 180, 52, 52, 52, 19, 19, 19, 1, 52, 52] 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: 829
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071174 none COCCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [46, 27, 15, 3, 1, 3, 1, 1, 1, 1, 11, 11, 34, 34, 52, 52, 52, 52, 52, 1, 46, 46, 46, 27, 27, 15, 15, 1, 1, 1, 11, 11, 11, 52, 1, 1] 201
rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 19, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 269
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071174 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071174
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071174/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071174
Building REAL250005071175
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071175'
/scratch/stefan/7916153/working/building/REAL250005071175 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071175

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071175/0 /scratch/stefan/7916153/working/building/REAL250005071175 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 296)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/296
`/scratch/stefan/7916153/working/3D/296' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2)C1)

`REAL250005071175.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071175.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071175/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071175 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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, 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
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 25, 25, 63, 63, 63, 63, 63, 1, 1, 1, 1, 4, 4, 18, 18, 1, 9, 9, 9, 63, 1, 1, 1, 18, 18, 18, 18, 18, 1, 1] 143
rigid atoms, others: [32, 1, 10, 11, 12, 13, 18, 23, 24, 25, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 19, 20, 21, 22, 26, 27, 28, 29, 30])
total number of confs: 166
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071175 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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, 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
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [33, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 63, 63, 63, 91, 91, 143, 143, 63, 33, 33, 33, 1, 63, 63, 63, 143, 143, 143, 143, 143, 63, 63] 143
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 22] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 483
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071175 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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, 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
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [81, 18, 81, 130, 130, 143, 143, 143, 143, 143, 18, 18, 8, 1, 8, 1, 1, 1, 18, 81, 81, 81, 143, 18, 18, 18, 1, 1, 1, 1, 1, 18, 18] 143
rigid atoms, others: [13, 15, 16, 17, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32])
total number of confs: 382
number of broken/clashed sets: 31
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071175 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071175
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071175/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071175
Building REAL250005071176
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071176'
/scratch/stefan/7916153/working/building/REAL250005071176 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071176

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071176/0 /scratch/stefan/7916153/working/building/REAL250005071176 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 297)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/297
`/scratch/stefan/7916153/working/3D/297' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCC2)C1)

`REAL250005071176.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071176.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071176/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071176 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 26, 26, 87, 87, 87, 87, 87, 1, 1, 1, 1, 6, 6, 24, 24, 24, 1, 9, 9, 9, 87, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 1, 1] 161
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 19, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 209
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071176 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [41, 10, 1, 10, 1, 1, 1, 1, 1, 1, 41, 87, 87, 87, 127, 127, 161, 161, 161, 87, 41, 41, 41, 1, 87, 87, 87, 161, 161, 161, 161, 161, 161, 161, 87, 87] 161
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 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: 517
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071176 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [78, 24, 78, 133, 133, 161, 161, 161, 161, 161, 24, 24, 8, 1, 8, 1, 1, 1, 1, 24, 78, 78, 78, 161, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 24, 24] 161
rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35])
total number of confs: 405
number of broken/clashed sets: 31
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071176 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071176
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071176/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071176
Building REAL250005071177
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071177'
/scratch/stefan/7916153/working/building/REAL250005071177 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071177

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071177/0 /scratch/stefan/7916153/working/building/REAL250005071177 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 298)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/298
`/scratch/stefan/7916153/working/3D/298' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCCC2)C1)

`REAL250005071177.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071177.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071177/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071177 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7, 7]
0  hydrogens 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, 31, 31, 91, 91, 91, 91, 91, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 1, 9, 9, 9, 91, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1] 201
rigid atoms, others: [1, 37, 38, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 226
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071177 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7, 7]
0  hydrogens 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, 10, 1, 10, 1, 1, 1, 1, 1, 1, 39, 91, 91, 91, 130, 130, 201, 201, 201, 201, 91, 39, 39, 39, 1, 91, 91, 91, 201, 201, 201, 201, 201, 201, 201, 201, 201, 91, 91] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 643
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071177 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7, 7]
0  hydrogens 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, 28, 87, 173, 173, 201, 201, 201, 201, 201, 28, 28, 8, 1, 8, 1, 1, 1, 1, 1, 28, 87, 87, 87, 201, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 201
rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38])
total number of confs: 499
number of broken/clashed sets: 82
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071177 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071177
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071177/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071177
Building REAL250005071178
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071178'
/scratch/stefan/7916153/working/building/REAL250005071178 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071178

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071178/0 /scratch/stefan/7916153/working/building/REAL250005071178 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 299)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/299
`/scratch/stefan/7916153/working/3D/299' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2CC2)C1)

`REAL250005071178.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071178.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071178/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071178 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 19, 19, 52, 52, 52, 52, 52, 1, 1, 1, 1, 6, 6, 27, 44, 44, 1, 7, 7, 7, 52, 1, 1, 1, 27, 27, 44, 44, 44, 44, 44, 1, 1] 201
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 19, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 252
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071178 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 52, 52, 52, 79, 79, 143, 201, 201, 52, 29, 29, 29, 1, 52, 52, 52, 143, 143, 201, 201, 201, 201, 201, 52, 52] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 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: 806
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071178 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [114, 44, 114, 179, 179, 201, 201, 201, 201, 201, 44, 44, 19, 3, 19, 1, 1, 1, 1, 44, 114, 114, 114, 201, 44, 44, 44, 3, 3, 1, 1, 1, 1, 1, 44, 44] 201
rigid atoms, others: [32, 33, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35])
total number of confs: 532
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071178 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071178
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071178/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071178
Building REAL250005071179
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071179'
/scratch/stefan/7916153/working/building/REAL250005071179 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071179

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071179/0 /scratch/stefan/7916153/working/building/REAL250005071179 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 300)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/300
`/scratch/stefan/7916153/working/3D/300' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)F)C1)

`REAL250005071179.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071179.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071179/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071179 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)F)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 15, 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, 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]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 18, 18, 30, 30, 30, 30, 30, 1, 1, 1, 1, 3, 3, 12, 12, 12, 1, 8, 8, 8, 30, 1, 1, 1, 12, 12, 12, 12, 12, 12, 1, 1] 69
rigid atoms, others: [1, 34, 33, 10, 11, 12, 13, 19, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32])
total number of confs: 104
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071179 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)F)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 15, 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, 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]
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: [20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 30, 30, 30, 42, 42, 69, 69, 69, 30, 20, 20, 20, 1, 30, 30, 30, 69, 69, 69, 69, 69, 69, 30, 30] 69
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 283
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071179 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071179
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071179/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071179
Building REAL250005071180
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071180'
/scratch/stefan/7916153/working/building/REAL250005071180 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071180

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071180/0 /scratch/stefan/7916153/working/building/REAL250005071180 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 301)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/301
`/scratch/stefan/7916153/working/3D/301' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(F)F)C1)

`REAL250005071180.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071180.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071180/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071180 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(F)F)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
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, 24, 24, 24, 24, 24, 1, 1, 1, 1, 5, 5, 19, 19, 19, 1, 7, 7, 7, 24, 1, 1, 1, 19, 19, 19, 1, 1] 54
rigid atoms, others: [1, 10, 11, 12, 13, 19, 24, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29])
total number of confs: 110
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071180 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(F)F)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
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: [20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 24, 24, 24, 27, 27, 54, 54, 54, 24, 20, 20, 20, 1, 24, 24, 24, 54, 54, 54, 24, 24] 54
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 205
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071180 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071180
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071180/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071180
Building REAL250005071181
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071181'
/scratch/stefan/7916153/working/building/REAL250005071181 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071181

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071181/0 /scratch/stefan/7916153/working/building/REAL250005071181 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 302)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/302
`/scratch/stefan/7916153/working/3D/302' -> `0.mol2'
Preparing input files

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

`REAL250005071181.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071181.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071181/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071181 none COCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 195, 89, 64, 89, 64, 64, 22, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 64, 201, 201, 201, 195, 195, 64, 64, 64, 22, 22, 22, 1, 64, 64] 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])
total number of confs: 755
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071181 none COCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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: [73, 25, 6, 1, 6, 1, 1, 1, 1, 11, 11, 37, 37, 64, 64, 64, 64, 64, 1, 73, 73, 73, 25, 25, 1, 1, 1, 11, 11, 11, 64, 1, 1] 201
rigid atoms, others: [32, 3, 5, 6, 7, 8, 18, 24, 25, 26, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 276
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071181 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071181
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071181/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071181
Building REAL250005071182
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071182'
/scratch/stefan/7916153/working/building/REAL250005071182 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071182

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071182/0 /scratch/stefan/7916153/working/building/REAL250005071182 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 303)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/303
`/scratch/stefan/7916153/working/3D/303' -> `0.mol2'
Preparing input files

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

`REAL250005071182.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071182.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071182/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071182 none CCCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 84, 61, 84, 61, 61, 23, 9, 23, 1, 9, 1, 1, 1, 1, 1, 1, 61, 201, 201, 201, 201, 201, 185, 185, 61, 61, 61, 23, 23, 23, 1, 61, 61] 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: 809
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071182 none CCCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 21, 5, 1, 5, 1, 1, 1, 1, 10, 10, 35, 35, 61, 61, 61, 61, 61, 1, 34, 34, 34, 34, 34, 21, 21, 1, 1, 1, 10, 10, 10, 61, 1, 1] 201
rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 18, 26, 27, 28] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32])
total number of confs: 299
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071182 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071182
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071182/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071182
Building REAL250005071183
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071183'
/scratch/stefan/7916153/working/building/REAL250005071183 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071183

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071183/0 /scratch/stefan/7916153/working/building/REAL250005071183 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 304)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/304
`/scratch/stefan/7916153/working/3D/304' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CC=CO2)C1)

`REAL250005071183.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071183.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071183/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071183 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CC=CO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 21, 21, 41, 41, 41, 41, 41, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 1, 9, 9, 9, 41, 1, 1, 1, 17, 16, 17, 1, 1] 88
rigid atoms, others: [32, 1, 10, 11, 12, 13, 20, 25, 26, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 116
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071183 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CC=CO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 41, 41, 41, 61, 61, 88, 88, 88, 88, 41, 26, 26, 26, 1, 41, 41, 41, 88, 88, 88, 41, 41] 88
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 235
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071183 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CC=CO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [45, 17, 45, 74, 74, 88, 88, 88, 88, 88, 17, 16, 8, 1, 8, 1, 1, 1, 1, 1, 17, 45, 45, 45, 88, 17, 16, 16, 1, 1, 1, 17, 17] 88
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32])
total number of confs: 224
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071183 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071183
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071183/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071183
Building REAL250005071184
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071184'
/scratch/stefan/7916153/working/building/REAL250005071184 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071184

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071184/0 /scratch/stefan/7916153/working/building/REAL250005071184 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 305)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/305
`/scratch/stefan/7916153/working/3D/305' -> `0.mol2'
Preparing input files

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

`REAL250005071184.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071184.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071184/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071184 none CC(=O)NCC(=O)N1CC(N(C)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 189, 85, 50, 85, 50, 50, 19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 50, 201, 201, 201, 201, 189, 189, 50, 50, 50, 19, 19, 19, 1, 50, 50] 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: 781
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071184 none CC(=O)NCC(=O)N1CC(N(C)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 17, 3, 1, 3, 1, 1, 1, 1, 11, 11, 34, 34, 50, 50, 50, 50, 50, 1, 51, 51, 51, 50, 17, 17, 1, 1, 1, 11, 11, 11, 50, 1, 1] 201
rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 260
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071184 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071184
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071184/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071184
Building REAL250005071185
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071185'
/scratch/stefan/7916153/working/building/REAL250005071185 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071185

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071185/0 /scratch/stefan/7916153/working/building/REAL250005071185 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 306)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/306
`/scratch/stefan/7916153/working/3D/306' -> `0.mol2'
Preparing input files

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

`REAL250005071185.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071185.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071185/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071185 none CC(C)CC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 191, 201, 123, 84, 123, 84, 84, 34, 10, 34, 1, 10, 1, 1, 1, 1, 1, 1, 84, 201, 201, 201, 201, 201, 201, 201, 191, 191, 84, 84, 84, 34, 34, 34, 1, 84, 84] 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: 808
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071185 none CC(C)CC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 22, 28, 7, 1, 7, 1, 1, 1, 1, 11, 11, 41, 41, 84, 84, 84, 84, 84, 1, 28, 28, 28, 28, 28, 28, 28, 22, 22, 1, 1, 1, 11, 11, 11, 84, 1, 1] 201
rigid atoms, others: [4, 37, 6, 7, 8, 9, 19, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35])
total number of confs: 306
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071185 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071185
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071185/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071185
Building REAL250005071186
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071186'
/scratch/stefan/7916153/working/building/REAL250005071186 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071186

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071186/0 /scratch/stefan/7916153/working/building/REAL250005071186 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 307)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/307
`/scratch/stefan/7916153/working/3D/307' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071186.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071186.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071186/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071186 none CC1CC1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 7, 1, 7, 1, 1, 1, 1, 11, 11, 42, 42, 92, 92, 92, 92, 92, 1, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 11, 11, 11, 92, 1, 1] 201
rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 19, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 239
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071186 none CC1CC1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 25, 25, 25, 100, 100, 187, 187, 201, 201, 201, 201, 201, 25, 2, 2, 2, 1, 1, 1, 1, 25, 25, 25, 100, 100, 100, 201, 25, 25] 201
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: 529
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071186 none CC1CC1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 92, 132, 92, 92, 28, 9, 28, 1, 9, 1, 1, 1, 1, 1, 1, 92, 201, 201, 201, 201, 201, 201, 201, 92, 92, 92, 28, 28, 28, 1, 92, 92] 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: 651
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071186 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071186
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071186/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071186
Building REAL250005071187
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071187'
/scratch/stefan/7916153/working/building/REAL250005071187 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071187

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071187/0 /scratch/stefan/7916153/working/building/REAL250005071187 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 308)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/308
`/scratch/stefan/7916153/working/3D/308' -> `0.mol2'
Preparing input files

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

`REAL250005071187.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071187.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071187/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071187 none CCOCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 179, 62, 44, 62, 44, 44, 18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 44, 201, 201, 201, 201, 201, 179, 179, 44, 44, 44, 18, 18, 18, 1, 44, 44] 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: 729
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071187 none CCOCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 72, 22, 3, 1, 3, 1, 1, 1, 1, 9, 9, 29, 29, 44, 44, 44, 44, 44, 1, 77, 77, 77, 77, 77, 22, 22, 1, 1, 1, 9, 9, 9, 44, 1, 1] 201
rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 19, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 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
/scratch/stefan/7916153/working/building/REAL250005071187 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071187
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071187/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071187
Building REAL250005071188
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071188'
/scratch/stefan/7916153/working/building/REAL250005071188 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071188

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071188/0 /scratch/stefan/7916153/working/building/REAL250005071188 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 309)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/309
`/scratch/stefan/7916153/working/3D/309' -> `0.mol2'
Preparing input files

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

`REAL250005071188.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071188.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071188/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071188 none CC(C)=CC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 125, 94, 125, 94, 94, 37, 11, 37, 1, 11, 1, 1, 1, 1, 1, 1, 94, 201, 201, 201, 201, 201, 201, 201, 94, 94, 94, 37, 37, 37, 1, 94, 94] 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: 637
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071188 none CC(C)=CC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 7, 1, 7, 1, 1, 1, 1, 11, 11, 41, 41, 94, 94, 94, 94, 94, 1, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 11, 11, 11, 94, 1, 1] 201
rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 19, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 237
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071188 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071188
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071188/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071188
Building REAL250005071189
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071189'
/scratch/stefan/7916153/working/building/REAL250005071189 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071189

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071189/0 /scratch/stefan/7916153/working/building/REAL250005071189 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 310)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/310
`/scratch/stefan/7916153/working/3D/310' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCCO2)C1)

`REAL250005071189.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071189.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071189/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071189 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCCO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 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, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 22, 22, 49, 49, 49, 49, 49, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 1, 9, 9, 9, 49, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 1, 1] 141
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 150
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071189 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCCO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 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, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [32, 10, 1, 10, 1, 1, 1, 1, 1, 1, 32, 49, 49, 49, 71, 71, 141, 141, 141, 141, 49, 32, 32, 32, 1, 49, 49, 49, 141, 141, 141, 141, 141, 141, 141, 49, 49] 141
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 431
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071189 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCCO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 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, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [75, 23, 75, 123, 123, 141, 141, 141, 141, 141, 23, 23, 11, 1, 11, 1, 1, 1, 1, 1, 23, 75, 75, 75, 141, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 23, 23] 141
rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36])
total number of confs: 368
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071189 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071189
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071189/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071189
Building REAL250005071190
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071190'
/scratch/stefan/7916153/working/building/REAL250005071190 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071190

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071190/0 /scratch/stefan/7916153/working/building/REAL250005071190 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 311)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/311
`/scratch/stefan/7916153/working/3D/311' -> `0.mol2'
Preparing input files

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

`REAL250005071190.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071190.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071190/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071190 none CSCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 162, 81, 56, 81, 56, 56, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 162, 162, 56, 56, 56, 21, 21, 21, 1, 56, 56] 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])
total number of confs: 726
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071190 none CSCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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: [60, 20, 5, 1, 5, 1, 1, 1, 1, 10, 10, 33, 33, 56, 56, 56, 56, 56, 1, 60, 60, 60, 20, 20, 1, 1, 1, 10, 10, 10, 56, 1, 1] 201
rigid atoms, others: [32, 3, 5, 6, 7, 8, 18, 24, 25, 26, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 230
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071190 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071190
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071190/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071190
Building REAL250005071191
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071191'
/scratch/stefan/7916153/working/building/REAL250005071191 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071191

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071191/0 /scratch/stefan/7916153/working/building/REAL250005071191 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 312)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/312
`/scratch/stefan/7916153/working/3D/312' -> `0.mol2'
Preparing input files

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

`REAL250005071191.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071191.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071191/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071191 none CSCCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 136, 136, 71, 51, 71, 51, 51, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 136, 136, 136, 136, 51, 51, 51, 20, 20, 20, 1, 51, 51] 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: 636
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071191 none CSCCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 17, 15, 3, 1, 3, 1, 1, 1, 1, 10, 10, 33, 33, 51, 51, 51, 51, 51, 1, 47, 47, 47, 17, 17, 15, 15, 1, 1, 1, 10, 10, 10, 51, 1, 1] 201
rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 19, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 217
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071191 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071191
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071191/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071191
Building REAL250005071192
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071192'
/scratch/stefan/7916153/working/building/REAL250005071192 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071192

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071192/0 /scratch/stefan/7916153/working/building/REAL250005071192 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 313)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/313
`/scratch/stefan/7916153/working/3D/313' -> `0.mol2'
Preparing input files

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

`REAL250005071192.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071192.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071192/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071192 none CC(C)CCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 198, 201, 178, 76, 53, 76, 53, 53, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 53, 201, 201, 199, 201, 201, 201, 201, 198, 198, 178, 178, 53, 53, 53, 19, 19, 19, 1, 53, 53] 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: 836
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071192 none CC(C)CCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 34, 19, 4, 1, 4, 1, 1, 1, 1, 9, 9, 34, 34, 53, 53, 53, 53, 53, 1, 34, 34, 30, 34, 34, 34, 34, 25, 25, 19, 19, 1, 1, 1, 9, 9, 9, 53, 1, 1] 201
rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 39, 40, 20] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 283
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071192 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071192
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071192/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071192
Building REAL250005071193
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071193'
/scratch/stefan/7916153/working/building/REAL250005071193 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071193

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071193/0 /scratch/stefan/7916153/working/building/REAL250005071193 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 314)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/314
`/scratch/stefan/7916153/working/3D/314' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CC=CN2)C1)

`REAL250005071193.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071193.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071193/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071193 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CC=CN2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 19, 19, 37, 37, 37, 37, 37, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 1, 7, 7, 7, 37, 1, 1, 1, 26, 25, 26, 26, 1, 1] 96
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 115
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071193 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CC=CN2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 37, 37, 37, 53, 53, 96, 96, 96, 96, 37, 23, 23, 23, 1, 37, 37, 37, 96, 96, 96, 96, 37, 37] 96
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 244
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071193 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CC=CN2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [61, 26, 61, 80, 80, 96, 96, 96, 96, 96, 26, 26, 11, 1, 11, 1, 1, 1, 1, 1, 26, 61, 61, 61, 96, 26, 26, 26, 1, 1, 1, 1, 26, 26] 96
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 243
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071193 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071193
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071193/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071193
Building REAL250005071194
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071194'
/scratch/stefan/7916153/working/building/REAL250005071194 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071194

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071194/0 /scratch/stefan/7916153/working/building/REAL250005071194 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 315)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/315
`/scratch/stefan/7916153/working/3D/315' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=COC=C2)C1)

`REAL250005071194.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071194.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071194/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071194 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=COC=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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, 7]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 18, 18, 40, 40, 40, 40, 40, 1, 1, 1, 1, 5, 5, 23, 23, 23, 23, 1, 6, 6, 6, 40, 1, 1, 1, 23, 23, 23, 1, 1] 110
rigid atoms, others: [32, 1, 10, 11, 12, 13, 20, 25, 26, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 112
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071194 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=COC=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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, 7]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [27, 8, 1, 8, 1, 1, 1, 1, 1, 1, 27, 40, 40, 40, 54, 54, 110, 110, 110, 110, 40, 27, 27, 27, 1, 40, 40, 40, 110, 110, 110, 40, 40] 110
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 264
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071194 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=COC=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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, 7]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [62, 23, 62, 88, 88, 110, 110, 110, 110, 110, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 23, 62, 62, 62, 110, 23, 23, 23, 1, 1, 1, 23, 23] 110
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32])
total number of confs: 279
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071194 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071194
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071194/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071194
Building REAL250005071195
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071195'
/scratch/stefan/7916153/working/building/REAL250005071195 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071195

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071195/0 /scratch/stefan/7916153/working/building/REAL250005071195 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 316)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/316
`/scratch/stefan/7916153/working/3D/316' -> `0.mol2'
Preparing input files

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

`REAL250005071195.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071195.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071195/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071195 none CCCCCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
179  conformations in input
total number of sets (complete confs): 179
using faster count positions algorithm for large data
unique positions, atoms: [179, 179, 179, 157, 58, 40, 58, 40, 40, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 40, 179, 179, 179, 179, 179, 179, 179, 179, 179, 157, 157, 40, 40, 40, 13, 13, 13, 1, 40, 40] 179
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: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071195 none CCCCCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
179  conformations in input
total number of sets (complete confs): 179
using faster count positions algorithm for large data
unique positions, atoms: [24, 29, 24, 16, 2, 1, 2, 1, 1, 1, 1, 7, 7, 25, 25, 40, 40, 40, 40, 40, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 16, 1, 1, 1, 7, 7, 7, 40, 1, 1] 179
rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 39, 40, 20] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 279
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071195 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071195
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071195/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071195
Building REAL250005071196
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071196'
/scratch/stefan/7916153/working/building/REAL250005071196 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071196

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071196/0 /scratch/stefan/7916153/working/building/REAL250005071196 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 317)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/317
`/scratch/stefan/7916153/working/3D/317' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC(C)(C)C)C1)

`REAL250005071196.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071196.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071196/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071196 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC(C)(C)C)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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, 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: [9, 1, 9, 22, 22, 49, 49, 49, 49, 49, 1, 1, 1, 1, 7, 7, 14, 21, 21, 21, 1, 9, 9, 9, 49, 1, 1, 1, 14, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1] 119
rigid atoms, others: [1, 39, 40, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 176
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071196 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC(C)(C)C)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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, 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: [28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 49, 49, 49, 72, 72, 116, 119, 119, 119, 49, 28, 28, 28, 1, 49, 49, 49, 116, 116, 119, 119, 119, 119, 119, 119, 119, 119, 119, 49, 49] 119
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 456
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071196 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071196
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071196/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071196
Building REAL250005071197
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071197'
/scratch/stefan/7916153/working/building/REAL250005071197 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071197

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071197/0 /scratch/stefan/7916153/working/building/REAL250005071197 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 318)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/318
`/scratch/stefan/7916153/working/3D/318' -> `0.mol2'
Preparing input files

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

`REAL250005071197.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071197.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071197/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071197 none CCCCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 190, 183, 66, 49, 66, 49, 49, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 49, 200, 201, 201, 201, 201, 190, 190, 183, 183, 49, 49, 49, 19, 19, 19, 1, 49, 49] 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: 809
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071197 none CCCCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [43, 25, 17, 3, 1, 3, 1, 1, 1, 1, 9, 9, 32, 32, 49, 49, 49, 49, 49, 1, 43, 45, 45, 45, 45, 31, 31, 17, 17, 1, 1, 1, 9, 9, 9, 49, 1, 1] 201
rigid atoms, others: [4, 37, 6, 7, 8, 9, 19, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35])
total number of confs: 346
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071197 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071197
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071197/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071197
Building REAL250005071198
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071198'
/scratch/stefan/7916153/working/building/REAL250005071198 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071198

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071198/0 /scratch/stefan/7916153/working/building/REAL250005071198 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 319)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/319
`/scratch/stefan/7916153/working/3D/319' -> `0.mol2'
Preparing input files

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

`REAL250005071198.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071198.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071198/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071198 none CC(C)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [140, 126, 140, 86, 126, 86, 86, 33, 10, 33, 1, 10, 1, 1, 1, 1, 1, 1, 86, 140, 140, 140, 140, 140, 140, 140, 86, 86, 86, 33, 33, 33, 1, 86, 86] 140
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: 469
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071198 none CC(C)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [17, 6, 17, 1, 6, 1, 1, 1, 1, 11, 11, 41, 41, 86, 86, 86, 86, 86, 1, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 11, 11, 11, 86, 1, 1] 140
rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 18, 26, 27, 28] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32])
total number of confs: 224
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071198 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071198
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071198/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071198
Building REAL250005071199
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071199'
/scratch/stefan/7916153/working/building/REAL250005071199 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071199

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071199/0 /scratch/stefan/7916153/working/building/REAL250005071199 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 320)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/320
`/scratch/stefan/7916153/working/3D/320' -> `0.mol2'
Preparing input files

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

`REAL250005071199.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071199.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071199/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071199 none CCC(C)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 119, 78, 119, 58, 78, 58, 58, 23, 8, 23, 1, 8, 1, 1, 1, 1, 1, 1, 58, 126, 126, 126, 126, 126, 119, 119, 119, 119, 58, 58, 58, 23, 23, 23, 1, 58, 58] 126
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: 471
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071199 none CCC(C)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 17, 6, 17, 1, 6, 1, 1, 1, 1, 7, 7, 33, 33, 58, 58, 58, 58, 58, 1, 27, 27, 27, 27, 27, 17, 17, 17, 17, 1, 1, 1, 7, 7, 7, 58, 1, 1] 126
rigid atoms, others: [4, 37, 6, 7, 8, 9, 19, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35])
total number of confs: 249
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071199 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071199
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071199/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071199
Building REAL250005071200
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071200'
/scratch/stefan/7916153/working/building/REAL250005071200 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071200

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071200/0 /scratch/stefan/7916153/working/building/REAL250005071200 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 321)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/321
`/scratch/stefan/7916153/working/3D/321' -> `0.mol2'
Preparing input files

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

`REAL250005071200.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071200.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071200/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071200 none CCC(CC)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [188, 168, 113, 168, 184, 79, 113, 79, 79, 28, 10, 28, 1, 10, 1, 1, 1, 1, 1, 1, 79, 191, 191, 191, 191, 191, 168, 188, 188, 188, 188, 188, 79, 79, 79, 28, 28, 28, 1, 79, 79] 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: 918
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071200 none CCC(CC)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 7, 16, 21, 1, 7, 1, 1, 1, 1, 11, 11, 41, 41, 79, 79, 79, 79, 79, 1, 26, 26, 26, 26, 26, 16, 24, 24, 24, 24, 24, 1, 1, 1, 11, 11, 11, 79, 1, 1] 201
rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 39, 40, 20] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 340
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071200 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071200
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071200/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071200
Building REAL250005071201
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071201'
/scratch/stefan/7916153/working/building/REAL250005071201 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071201

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071201/0 /scratch/stefan/7916153/working/building/REAL250005071201 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 322)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/322
`/scratch/stefan/7916153/working/3D/322' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NNC=C2)C1)

`REAL250005071201.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071201.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071201/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071201 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NNC=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
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: [9, 1, 9, 21, 21, 37, 37, 37, 37, 37, 1, 1, 1, 1, 4, 4, 13, 13, 13, 13, 1, 9, 9, 9, 37, 1, 1, 1, 14, 13, 13, 1, 1] 73
rigid atoms, others: [32, 1, 10, 11, 12, 13, 20, 25, 26, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 102
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071201 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NNC=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
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: [23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 37, 37, 37, 49, 49, 73, 73, 73, 73, 37, 23, 23, 23, 1, 37, 37, 37, 73, 73, 73, 37, 37] 73
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071201 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NNC=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
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: [37, 13, 37, 63, 63, 73, 73, 73, 73, 73, 13, 13, 7, 1, 7, 1, 1, 1, 1, 1, 13, 37, 37, 37, 73, 13, 13, 13, 1, 1, 1, 13, 13] 73
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32])
total number of confs: 188
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071201 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071201/1 /scratch/stefan/7916153/working/building/REAL250005071201 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 323)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/323
`/scratch/stefan/7916153/working/3D/323' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CC=NN2)C1)

`REAL250005071201.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071201.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071201/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071201 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CC=NN2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [6, 1, 6, 18, 18, 42, 42, 42, 42, 42, 1, 1, 1, 1, 5, 5, 26, 26, 26, 26, 1, 6, 6, 6, 42, 1, 1, 1, 26, 26, 26, 1, 1] 98
rigid atoms, others: [32, 1, 10, 11, 12, 13, 20, 25, 26, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 116
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071201 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CC=NN2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 42, 42, 42, 60, 60, 98, 98, 98, 98, 42, 25, 25, 25, 1, 42, 42, 42, 98, 98, 98, 42, 42] 98
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 257
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071201 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CC=NN2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [60, 26, 60, 82, 82, 98, 98, 98, 98, 98, 26, 26, 11, 1, 11, 1, 1, 1, 1, 1, 26, 60, 60, 60, 98, 26, 26, 26, 1, 1, 1, 26, 26] 98
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32])
total number of confs: 252
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071201 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071201
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071201/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071201/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071201
Building REAL250005071202
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071202'
/scratch/stefan/7916153/working/building/REAL250005071202 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071202

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071202/0 /scratch/stefan/7916153/working/building/REAL250005071202 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 324)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/324
`/scratch/stefan/7916153/working/3D/324' -> `0.mol2'
Preparing input files

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

`REAL250005071202.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071202.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071202/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071202 none CSC(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 140, 95, 140, 68, 95, 68, 68, 25, 10, 25, 1, 10, 1, 1, 1, 1, 1, 1, 68, 176, 176, 176, 140, 140, 140, 140, 68, 68, 68, 25, 25, 25, 1, 68, 68] 176
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: 565
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071202 none CSC(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [58, 22, 7, 22, 1, 7, 1, 1, 1, 1, 8, 8, 34, 34, 68, 68, 68, 68, 68, 1, 56, 58, 58, 22, 22, 22, 22, 1, 1, 1, 8, 8, 8, 68, 1, 1] 176
rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 19, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 260
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071202 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071202
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071202/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071202
Building REAL250005071203
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071203'
/scratch/stefan/7916153/working/building/REAL250005071203 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071203

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071203/0 /scratch/stefan/7916153/working/building/REAL250005071203 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 325)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/325
`/scratch/stefan/7916153/working/3D/325' -> `0.mol2'
Preparing input files

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

`REAL250005071203.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071203.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071203/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071203 none CCOC(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 189, 98, 189, 68, 98, 68, 68, 25, 8, 25, 1, 8, 1, 1, 1, 1, 1, 1, 68, 201, 201, 201, 201, 201, 189, 189, 189, 189, 68, 68, 68, 25, 25, 25, 1, 68, 68] 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: 737
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071203 none CCOC(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 53, 28, 7, 28, 1, 7, 1, 1, 1, 1, 7, 7, 32, 32, 68, 68, 68, 68, 68, 1, 59, 59, 59, 59, 59, 28, 28, 28, 28, 1, 1, 1, 7, 7, 7, 68, 1, 1] 201
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 300
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071203 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071203
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071203/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071203
Building REAL250005071204
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071204'
/scratch/stefan/7916153/working/building/REAL250005071204 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071204

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071204/0 /scratch/stefan/7916153/working/building/REAL250005071204 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 326)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/326
`/scratch/stefan/7916153/working/3D/326' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CNN=C2)C1)

`REAL250005071204.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071204.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071204/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071204 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CNN=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 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, 3, 7, 7, 7, 7, 6, 7, 7, 4, 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: [6, 1, 6, 18, 18, 35, 35, 35, 35, 35, 1, 1, 1, 1, 5, 5, 14, 14, 14, 14, 1, 6, 6, 6, 35, 1, 1, 1, 14, 14, 14, 1, 1] 57
rigid atoms, others: [32, 1, 10, 11, 12, 13, 20, 25, 26, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 97
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071204 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CNN=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 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, 3, 7, 7, 7, 7, 6, 7, 7, 4, 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, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 35, 35, 35, 48, 48, 57, 57, 57, 57, 35, 22, 22, 22, 1, 35, 35, 35, 57, 57, 57, 35, 35] 57
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 173
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071204 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CNN=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 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, 3, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [34, 16, 34, 49, 49, 62, 62, 62, 62, 62, 16, 16, 8, 1, 8, 1, 1, 1, 1, 1, 16, 34, 34, 34, 62, 16, 16, 16, 1, 1, 1, 16, 16] 62
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32])
total number of confs: 156
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071204 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071204
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071204/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071204
Building REAL250005071205
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071205'
/scratch/stefan/7916153/working/building/REAL250005071205 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071205

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071205/0 /scratch/stefan/7916153/working/building/REAL250005071205 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 327)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/327
`/scratch/stefan/7916153/working/3D/327' -> `0.mol2'
Preparing input files

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

`REAL250005071205.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071205.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071205/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071205 none COCCCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 30, 22, 30, 22, 22, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 22, 67, 67, 67, 67, 67, 67, 67, 67, 67, 22, 22, 22, 14, 14, 14, 1, 22, 22] 67
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: 250
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071205 none COCCCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 16, 15, 13, 2, 1, 2, 1, 1, 1, 1, 6, 6, 16, 16, 22, 22, 22, 22, 22, 1, 18, 18, 18, 16, 16, 15, 15, 13, 13, 1, 1, 1, 6, 6, 6, 22, 1, 1] 67
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 118
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071205 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071205
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071205/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071205
Building REAL250005071206
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071206'
/scratch/stefan/7916153/working/building/REAL250005071206 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071206

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071206/0 /scratch/stefan/7916153/working/building/REAL250005071206 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 328)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/328
`/scratch/stefan/7916153/working/3D/328' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NOC=C2)C1)

`REAL250005071206.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071206.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071206/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071206 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NOC=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 20, 20, 36, 36, 36, 36, 36, 1, 1, 1, 1, 5, 5, 20, 20, 20, 20, 1, 8, 8, 8, 36, 1, 1, 1, 20, 20, 1, 1] 80
rigid atoms, others: [1, 10, 11, 12, 13, 20, 25, 26, 27, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29])
total number of confs: 107
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071206 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NOC=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 36, 36, 36, 51, 51, 80, 80, 80, 80, 36, 23, 23, 23, 1, 36, 36, 36, 80, 80, 36, 36] 80
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 210
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071206 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NOC=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [46, 20, 46, 70, 70, 80, 80, 80, 80, 80, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 20, 46, 46, 46, 80, 20, 20, 20, 1, 1, 20, 20] 80
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 200
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071206 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071206
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071206/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071206
Building REAL250005071207
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071207'
/scratch/stefan/7916153/working/building/REAL250005071207 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071207

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071207/0 /scratch/stefan/7916153/working/building/REAL250005071207 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 329)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/329
`/scratch/stefan/7916153/working/3D/329' -> `0.mol2'
Preparing input files

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

`REAL250005071207.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071207.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071207/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071207 none CCC=C(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [150, 142, 142, 72, 142, 42, 72, 42, 42, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 42, 150, 150, 150, 150, 150, 142, 142, 142, 142, 42, 42, 42, 14, 14, 14, 1, 42, 42] 150
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: 477
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071207 none CCC=C(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [30, 19, 19, 4, 19, 1, 4, 1, 1, 1, 1, 8, 8, 26, 26, 42, 42, 42, 42, 42, 1, 30, 30, 30, 30, 30, 19, 19, 19, 19, 1, 1, 1, 8, 8, 8, 42, 1, 1] 150
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 187
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071207 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071207
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071207/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071207
Building REAL250005071208
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071208'
/scratch/stefan/7916153/working/building/REAL250005071208 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071208

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071208/0 /scratch/stefan/7916153/working/building/REAL250005071208 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 330)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/330
`/scratch/stefan/7916153/working/3D/330' -> `0.mol2'
Preparing input files

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

`REAL250005071208.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071208.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071208/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071208 none COC(C)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 133, 77, 133, 58, 77, 58, 58, 22, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 58, 136, 136, 136, 133, 133, 133, 133, 58, 58, 58, 22, 22, 22, 1, 58, 58] 136
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: 505
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071208 none COC(C)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 24, 7, 24, 1, 7, 1, 1, 1, 1, 7, 7, 31, 31, 58, 58, 58, 58, 58, 1, 43, 43, 43, 24, 24, 24, 24, 1, 1, 1, 7, 7, 7, 58, 1, 1] 136
rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 19, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 227
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071208 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071208
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071208/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071208
Building REAL250005071209
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071209'
/scratch/stefan/7916153/working/building/REAL250005071209 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071209

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071209/0 /scratch/stefan/7916153/working/building/REAL250005071209 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 331)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/331
`/scratch/stefan/7916153/working/3D/331' -> `0.mol2'
Preparing input files

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

`REAL250005071209.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071209.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071209/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071209 none CC(C)OCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 183, 201, 111, 40, 30, 40, 30, 30, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 30, 201, 201, 201, 201, 201, 201, 201, 111, 111, 30, 30, 30, 15, 15, 15, 1, 30, 30] 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: 648
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071209 none CC(C)OCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 76, 95, 20, 3, 1, 3, 1, 1, 1, 1, 9, 9, 20, 20, 30, 30, 30, 30, 30, 1, 95, 95, 95, 95, 95, 95, 95, 20, 20, 1, 1, 1, 9, 9, 9, 30, 1, 1] 201
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 317
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071209 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071209
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071209/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071209
Building REAL250005071210
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071210'
/scratch/stefan/7916153/working/building/REAL250005071210 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071210

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071210/0 /scratch/stefan/7916153/working/building/REAL250005071210 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 332)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/332
`/scratch/stefan/7916153/working/3D/332' -> `0.mol2'
Preparing input files

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

`REAL250005071210.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071210.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071210/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071210 none CCCOCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 143, 109, 38, 28, 38, 28, 28, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 28, 201, 201, 201, 201, 201, 160, 160, 109, 109, 28, 28, 28, 13, 13, 13, 1, 28, 28] 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: 814
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071210 none CCCOCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 52, 35, 16, 3, 1, 3, 1, 1, 1, 1, 9, 9, 19, 19, 28, 28, 28, 28, 28, 1, 89, 89, 89, 89, 89, 52, 52, 16, 16, 1, 1, 1, 9, 9, 9, 28, 1, 1] 201
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 402
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071210 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071210
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071210/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071210
Building REAL250005071211
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071211'
/scratch/stefan/7916153/working/building/REAL250005071211 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071211

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071211/0 /scratch/stefan/7916153/working/building/REAL250005071211 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 333)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/333
`/scratch/stefan/7916153/working/3D/333' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCOC2)C1)

`REAL250005071211.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071211.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071211/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071211 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCOC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 24, 24, 62, 62, 62, 62, 62, 1, 1, 1, 1, 5, 5, 25, 25, 25, 25, 1, 9, 9, 9, 62, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 1, 1] 155
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 180
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071211 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCOC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 62, 62, 62, 84, 84, 155, 155, 155, 155, 62, 34, 34, 34, 1, 62, 62, 62, 155, 155, 155, 155, 155, 155, 155, 62, 62] 155
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 501
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071211 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCOC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [79, 25, 79, 129, 129, 155, 155, 155, 155, 155, 25, 25, 8, 1, 8, 1, 1, 1, 1, 1, 25, 79, 79, 79, 155, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 25, 25] 155
rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36])
total number of confs: 393
number of broken/clashed sets: 37
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071211 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071211
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071211/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071211
Building REAL250005071212
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071212'
/scratch/stefan/7916153/working/building/REAL250005071212 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071212

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071212/0 /scratch/stefan/7916153/working/building/REAL250005071212 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 334)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/334
`/scratch/stefan/7916153/working/3D/334' -> `0.mol2'
Preparing input files

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

`REAL250005071212.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071212.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071212/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071212 none CCC(OC)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [188, 187, 87, 187, 198, 64, 87, 64, 64, 23, 8, 23, 1, 8, 1, 1, 1, 1, 1, 1, 64, 201, 201, 201, 201, 201, 187, 198, 198, 198, 64, 64, 64, 23, 23, 23, 1, 64, 64] 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: 906
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071212 none CCC(OC)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 19, 5, 19, 32, 1, 5, 1, 1, 1, 1, 10, 10, 36, 36, 64, 64, 64, 64, 64, 1, 34, 34, 34, 34, 34, 19, 32, 32, 32, 1, 1, 1, 10, 10, 10, 64, 1, 1] 201
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 326
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071212 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071212
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071212/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071212
Building REAL250005071213
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071213'
/scratch/stefan/7916153/working/building/REAL250005071213 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071213

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071213/0 /scratch/stefan/7916153/working/building/REAL250005071213 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 335)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/335
`/scratch/stefan/7916153/working/3D/335' -> `0.mol2'
Preparing input files

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

`REAL250005071213.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071213.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071213/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071213 none COC(C)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 164, 201, 60, 46, 60, 46, 46, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 46, 201, 201, 201, 201, 201, 201, 201, 164, 164, 46, 46, 46, 19, 19, 19, 1, 46, 46] 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: 825
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071213 none COC(C)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 41, 17, 40, 3, 1, 3, 1, 1, 1, 1, 9, 9, 30, 30, 46, 46, 46, 46, 46, 1, 58, 58, 58, 41, 41, 41, 41, 17, 17, 1, 1, 1, 9, 9, 9, 46, 1, 1] 201
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 317
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071213 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071213
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071213/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071213
Building REAL250005071214
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071214'
/scratch/stefan/7916153/working/building/REAL250005071214 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071214

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071214/0 /scratch/stefan/7916153/working/building/REAL250005071214 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 336)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/336
`/scratch/stefan/7916153/working/3D/336' -> `0.mol2'
Preparing input files

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

`REAL250005071214.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071214.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071214/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071214 none C=CCCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 66, 51, 66, 51, 51, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 201, 201, 185, 185, 51, 51, 51, 21, 21, 21, 1, 51, 51] 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: 795
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071214 none C=CCCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 28, 17, 3, 1, 3, 1, 1, 1, 1, 9, 9, 29, 29, 51, 51, 51, 51, 51, 1, 56, 56, 56, 28, 28, 17, 17, 1, 1, 1, 9, 9, 9, 51, 1, 1] 201
rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 19, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 312
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071214 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071214
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071214/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071214
Building REAL250005071215
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071215'
/scratch/stefan/7916153/working/building/REAL250005071215 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071215

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071215/0 /scratch/stefan/7916153/working/building/REAL250005071215 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 337)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/337
`/scratch/stefan/7916153/working/3D/337' -> `0.mol2'
Preparing input files

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

`REAL250005071215.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071215.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071215/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071215 none CCOCCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 199, 176, 64, 44, 64, 44, 44, 17, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 44, 201, 201, 201, 201, 201, 199, 199, 176, 176, 44, 44, 44, 17, 17, 17, 1, 44, 44] 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: 790
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071215 none CCOCCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 50, 27, 15, 3, 1, 3, 1, 1, 1, 1, 11, 11, 33, 33, 44, 44, 44, 44, 44, 1, 53, 53, 53, 53, 53, 27, 27, 15, 15, 1, 1, 1, 11, 11, 11, 44, 1, 1] 201
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 282
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071215 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071215
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071215/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071215
Building REAL250005071216
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071216'
/scratch/stefan/7916153/working/building/REAL250005071216 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071216

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071216/0 /scratch/stefan/7916153/working/building/REAL250005071216 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 338)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/338
`/scratch/stefan/7916153/working/3D/338' -> `0.mol2'
Preparing input files

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

`REAL250005071216.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071216.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071216/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071216 none COCC(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 157, 89, 157, 58, 89, 58, 58, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 200, 200, 157, 157, 157, 157, 58, 58, 58, 20, 20, 20, 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: 862
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071216 none COCC(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 39, 14, 5, 14, 1, 5, 1, 1, 1, 1, 7, 7, 30, 30, 58, 58, 58, 58, 58, 1, 69, 69, 69, 39, 39, 14, 14, 14, 14, 1, 1, 1, 7, 7, 7, 58, 1, 1] 201
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 316
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071216 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071216
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071216/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071216
Building REAL250005071217
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071217'
/scratch/stefan/7916153/working/building/REAL250005071217 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071217

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071217/0 /scratch/stefan/7916153/working/building/REAL250005071217 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 339)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/339
`/scratch/stefan/7916153/working/3D/339' -> `0.mol2'
Preparing input files

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

`REAL250005071217.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071217.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071217/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071217 none C=CCOCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 166, 133, 52, 37, 52, 37, 37, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 37, 201, 201, 201, 201, 201, 133, 133, 37, 37, 37, 16, 16, 16, 1, 37, 37] 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: 788
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071217 none C=CCOCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 52, 17, 9, 3, 1, 3, 1, 1, 1, 1, 9, 9, 23, 23, 37, 37, 37, 37, 37, 1, 75, 75, 75, 52, 52, 9, 9, 1, 1, 1, 9, 9, 9, 37, 1, 1] 201
rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 351
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071217 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071217
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071217/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071217
Building REAL250005071218
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071218'
/scratch/stefan/7916153/working/building/REAL250005071218 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071218

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071218/0 /scratch/stefan/7916153/working/building/REAL250005071218 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 340)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/340
`/scratch/stefan/7916153/working/3D/340' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=COC=N2)C1)

`REAL250005071218.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071218.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071218/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071218 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=COC=N2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 22, 22, 36, 36, 36, 36, 36, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 1, 9, 9, 9, 36, 1, 1, 1, 17, 17, 1, 1] 73
rigid atoms, others: [1, 10, 11, 12, 13, 20, 25, 26, 27, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29])
total number of confs: 107
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071218 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=COC=N2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 36, 36, 36, 56, 56, 73, 73, 73, 73, 36, 20, 20, 20, 1, 36, 36, 36, 73, 73, 36, 36] 73
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 209
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071218 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=COC=N2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [40, 18, 40, 64, 64, 73, 73, 73, 73, 73, 18, 17, 8, 1, 8, 1, 1, 1, 1, 1, 17, 40, 40, 40, 73, 18, 18, 18, 1, 1, 17, 17] 73
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 189
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071218 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071218
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071218/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071218
Building REAL250005071219
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071219'
/scratch/stefan/7916153/working/building/REAL250005071219 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071219

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071219/0 /scratch/stefan/7916153/working/building/REAL250005071219 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 341)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/341
`/scratch/stefan/7916153/working/3D/341' -> `0.mol2'
Preparing input files

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

`REAL250005071219.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071219.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071219/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071219 none CCCC(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 172, 102, 172, 63, 102, 63, 63, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 63, 201, 201, 201, 201, 197, 196, 196, 172, 172, 172, 172, 63, 63, 63, 21, 21, 21, 1, 63, 63] 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: 833
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071219 none CCCC(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 51, 22, 6, 22, 1, 6, 1, 1, 1, 1, 7, 7, 31, 31, 63, 63, 63, 63, 63, 1, 62, 62, 62, 62, 60, 53, 53, 22, 23, 23, 23, 1, 1, 1, 7, 7, 7, 63, 1, 1] 201
rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 39, 40, 20] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 399
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071219 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071219
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071219/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071219
Building REAL250005071220
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071220'
/scratch/stefan/7916153/working/building/REAL250005071220 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071220

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071220/0 /scratch/stefan/7916153/working/building/REAL250005071220 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 342)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/342
`/scratch/stefan/7916153/working/3D/342' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCC2CC2)C1)

`REAL250005071220.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071220.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071220/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071220 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCC2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 15, 15, 31, 31, 31, 31, 31, 1, 1, 1, 1, 3, 3, 17, 27, 56, 56, 1, 5, 5, 5, 31, 1, 1, 1, 17, 17, 33, 33, 56, 56, 56, 56, 56, 1, 1] 201
rigid atoms, others: [1, 37, 38, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 304
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071220 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCC2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 31, 31, 31, 43, 43, 131, 144, 201, 201, 31, 17, 17, 17, 1, 31, 31, 31, 131, 131, 146, 146, 201, 201, 201, 201, 201, 31, 31] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 826
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071220 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCC2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7, 7]
0  hydrogens 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, 56, 135, 195, 195, 201, 201, 201, 201, 201, 56, 56, 35, 7, 35, 3, 1, 1, 1, 1, 56, 135, 135, 135, 201, 56, 56, 56, 7, 7, 3, 3, 1, 1, 1, 1, 1, 56, 56] 201
rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38])
total number of confs: 594
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071220 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071220
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071220/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071220
Building REAL250005071221
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071221'
/scratch/stefan/7916153/working/building/REAL250005071221 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071221

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071221/0 /scratch/stefan/7916153/working/building/REAL250005071221 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 343)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/343
`/scratch/stefan/7916153/working/3D/343' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC=CC2)C1)

`REAL250005071221.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071221.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071221/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071221 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC=CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 1, 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, 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, 7]
0  hydrogens need rotated
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 24, 24, 60, 60, 60, 60, 60, 1, 1, 1, 1, 5, 5, 25, 25, 25, 25, 1, 9, 9, 9, 60, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 1, 1] 165
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 179
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071221 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC=CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 1, 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, 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, 7]
0  hydrogens need rotated
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [35, 10, 1, 10, 1, 1, 1, 1, 1, 1, 35, 60, 60, 60, 81, 81, 165, 165, 165, 165, 60, 35, 35, 35, 1, 60, 60, 60, 165, 165, 165, 165, 165, 165, 165, 60, 60] 165
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 521
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071221 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC=CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 1, 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, 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, 7]
0  hydrogens need rotated
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [83, 25, 83, 135, 135, 165, 165, 165, 165, 165, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 25, 83, 83, 83, 165, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 25, 25] 165
rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36])
total number of confs: 413
number of broken/clashed sets: 36
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071221 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071221
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071221/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071221
Building REAL250005071222
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071222'
/scratch/stefan/7916153/working/building/REAL250005071222 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071222

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071222/0 /scratch/stefan/7916153/working/building/REAL250005071222 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 344)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/344
`/scratch/stefan/7916153/working/3D/344' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2CCC2)C1)

`REAL250005071222.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071222.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071222/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071222 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 26, 26, 56, 56, 56, 56, 56, 1, 1, 1, 1, 6, 6, 20, 48, 48, 48, 1, 8, 8, 8, 56, 1, 1, 1, 20, 20, 48, 48, 48, 48, 48, 48, 48, 1, 1] 201
rigid atoms, others: [1, 37, 38, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 259
number of broken/clashed sets: 64
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071222 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 22, 56, 56, 56, 84, 84, 161, 201, 201, 201, 56, 22, 22, 22, 1, 56, 56, 56, 161, 161, 201, 201, 201, 201, 201, 201, 201, 56, 56] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 827
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071222 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [111, 48, 111, 192, 192, 201, 201, 201, 201, 201, 48, 48, 28, 6, 28, 1, 1, 1, 1, 1, 48, 111, 111, 111, 201, 48, 48, 48, 6, 6, 1, 1, 1, 1, 1, 1, 1, 48, 48] 201
rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38])
total number of confs: 577
number of broken/clashed sets: 64
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071222 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071222
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071222/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071222
Building REAL250005071223
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071223'
/scratch/stefan/7916153/working/building/REAL250005071223 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071223

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071223/0 /scratch/stefan/7916153/working/building/REAL250005071223 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 345)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/345
`/scratch/stefan/7916153/working/3D/345' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)C1CC1)

`REAL250005071223.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071223.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071223/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071223 none CC(C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', '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, 1, 11, 8, 5, 5, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [101, 78, 54, 78, 54, 54, 22, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 54, 101, 104, 104, 101, 101, 101, 101, 54, 54, 54, 22, 22, 22, 1, 54, 54, 104, 104, 104, 104, 104] 104
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, 36, 37, 38])
total number of confs: 371
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071223 none CC(C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', '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, 1, 11, 8, 5, 5, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 7, 1, 7, 1, 1, 1, 1, 8, 8, 32, 32, 54, 54, 54, 54, 54, 1, 19, 28, 28, 19, 19, 19, 19, 1, 1, 1, 8, 8, 8, 54, 1, 1, 28, 28, 28, 28, 28] 104
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 17, 25, 26, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 34, 35, 36, 37, 38])
total number of confs: 209
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071223 none CC(C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', '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, 1, 11, 8, 5, 5, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 16, 16, 28, 28, 28, 56, 56, 96, 96, 104, 104, 104, 104, 104, 28, 1, 1, 1, 7, 7, 7, 7, 28, 28, 28, 56, 56, 56, 104, 28, 28, 1, 1, 1, 1, 1] 104
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: 281
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071223 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071223
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071223/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071223
Building REAL250005071224
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071224'
/scratch/stefan/7916153/working/building/REAL250005071224 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071224

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071224/0 /scratch/stefan/7916153/working/building/REAL250005071224 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 346)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/346
`/scratch/stefan/7916153/working/3D/346' -> `0.mol2'
Preparing input files

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

`REAL250005071224.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071224.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071224/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071224 none CC=C(C)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 121, 201, 86, 121, 86, 86, 29, 10, 29, 1, 10, 1, 1, 1, 1, 1, 1, 86, 201, 201, 201, 201, 201, 201, 201, 86, 86, 86, 29, 29, 29, 1, 86, 86] 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: 669
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071224 none CC=C(C)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 6, 24, 1, 6, 1, 1, 1, 1, 11, 11, 42, 42, 86, 86, 86, 86, 86, 1, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 11, 11, 11, 86, 1, 1] 201
rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 19, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 228
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071224 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071224
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071224/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071224
Building REAL250005071225
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071225'
/scratch/stefan/7916153/working/building/REAL250005071225 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071225

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071225/0 /scratch/stefan/7916153/working/building/REAL250005071225 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 347)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/347
`/scratch/stefan/7916153/working/3D/347' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)C1)

`REAL250005071225.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071225.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071225/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071225 none CC1CC(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 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, 7, 6, 7, 7, 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: [24, 24, 24, 6, 1, 6, 1, 1, 1, 1, 10, 10, 41, 41, 100, 100, 100, 100, 100, 1, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 11, 11, 11, 100, 1, 1, 24, 24] 201
rigid atoms, others: [35, 4, 6, 7, 8, 9, 19, 36, 28, 29, 30] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 37, 38])
total number of confs: 252
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071225 none CC1CC(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 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, 7, 6, 7, 7, 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, 8, 8, 24, 24, 24, 92, 92, 179, 179, 201, 201, 201, 201, 201, 24, 1, 2, 2, 2, 1, 1, 1, 1, 24, 24, 24, 92, 92, 92, 201, 24, 24, 1, 1] 201
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: 517
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071225 none CC1CC(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 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, 7, 6, 7, 7, 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, 151, 100, 151, 100, 100, 34, 11, 34, 1, 11, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 201, 201, 201, 100, 100, 100, 34, 34, 34, 1, 100, 100, 201, 201] 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: 661
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071225 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071225
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071225/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071225
Building REAL250005071226
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071226'
/scratch/stefan/7916153/working/building/REAL250005071226 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071226

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071226/0 /scratch/stefan/7916153/working/building/REAL250005071226 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 348)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/348
`/scratch/stefan/7916153/working/3D/348' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=C2CCC2)C1)

`REAL250005071226.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071226.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071226/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071226 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=C2CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 20, 20, 46, 46, 46, 46, 46, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 1, 8, 8, 8, 46, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 1, 1] 151
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 142
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071226 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=C2CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [33, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 46, 46, 46, 67, 67, 151, 151, 151, 151, 46, 33, 33, 33, 1, 46, 46, 46, 151, 151, 151, 151, 151, 151, 151, 46, 46] 151
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 439
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071226 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=C2CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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, 7]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [85, 23, 85, 130, 130, 151, 151, 151, 151, 151, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 23, 85, 85, 85, 151, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 23, 23] 151
rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36])
total number of confs: 395
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071226 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071226
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071226/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071226
Building REAL250005071227
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071227'
/scratch/stefan/7916153/working/building/REAL250005071227 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071227

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071227/0 /scratch/stefan/7916153/working/building/REAL250005071227 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 349)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/349
`/scratch/stefan/7916153/working/3D/349' -> `0.mol2'
Preparing input files

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

`REAL250005071227.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071227.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071227/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071227 none CC(C)=C(F)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 110, 154, 80, 110, 80, 80, 29, 10, 29, 1, 10, 1, 1, 1, 1, 1, 1, 80, 154, 154, 154, 154, 154, 154, 80, 80, 80, 29, 29, 29, 1, 80, 80] 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: 489
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071227 none CC(C)=C(F)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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: [19, 19, 19, 7, 19, 1, 7, 1, 1, 1, 1, 11, 11, 41, 41, 80, 80, 80, 80, 80, 1, 19, 19, 19, 19, 19, 19, 1, 1, 1, 11, 11, 11, 80, 1, 1] 154
rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 205
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071227 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071227
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071227/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071227
Building REAL250005071228
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071228'
/scratch/stefan/7916153/working/building/REAL250005071228 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071228

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071228/0 /scratch/stefan/7916153/working/building/REAL250005071228 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 350)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/350
`/scratch/stefan/7916153/working/3D/350' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CCCC2)C1)

`REAL250005071228.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071228.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071228/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071228 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CCCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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, 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: [8, 1, 8, 22, 22, 51, 51, 51, 51, 51, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 1, 8, 8, 8, 51, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 1, 1] 92
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 130
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071228 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CCCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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, 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: [28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 51, 51, 51, 81, 81, 92, 92, 92, 92, 51, 28, 28, 28, 1, 51, 51, 51, 92, 92, 92, 92, 92, 92, 92, 51, 51] 92
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 261
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071228 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CCCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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, 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: [57, 18, 57, 87, 87, 92, 92, 92, 92, 92, 19, 19, 7, 1, 7, 1, 1, 1, 1, 1, 19, 57, 57, 57, 92, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 19, 19] 92
rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36])
total number of confs: 245
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071228 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071228
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071228/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071228
Building REAL250005071229
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071229'
/scratch/stefan/7916153/working/building/REAL250005071229 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071229

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071229/0 /scratch/stefan/7916153/working/building/REAL250005071229 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 351)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/351
`/scratch/stefan/7916153/working/3D/351' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2(C)C)C1)

`REAL250005071229.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071229.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071229/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071229 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2(C)C)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 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: [9, 1, 9, 31, 31, 83, 83, 83, 83, 83, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 1, 9, 9, 9, 83, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1] 173
rigid atoms, others: [1, 37, 38, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 197
number of broken/clashed sets: 71
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071229 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2(C)C)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 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: [37, 10, 1, 10, 1, 1, 1, 1, 1, 1, 37, 83, 83, 83, 122, 122, 173, 173, 173, 173, 83, 37, 37, 37, 1, 83, 83, 83, 173, 173, 173, 173, 173, 173, 173, 173, 173, 83, 83] 173
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 549
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071229 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2(C)C)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 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: [69, 22, 69, 149, 149, 173, 173, 173, 173, 173, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 22, 69, 69, 69, 173, 22, 22, 22, 1, 1, 1, 2, 2, 2, 2, 2, 2, 22, 22] 173
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 452
number of broken/clashed sets: 71
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071229 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071229
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071229/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071229
Building REAL250005071230
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071230'
/scratch/stefan/7916153/working/building/REAL250005071230 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071230

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071230/0 /scratch/stefan/7916153/working/building/REAL250005071230 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 352)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/352
`/scratch/stefan/7916153/working/3D/352' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2CC2(C)C)C1)

`REAL250005071230.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071230.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071230/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071230 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2CC2(C)C)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 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, 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, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 21, 21, 57, 57, 57, 57, 57, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 8, 8, 8, 57, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1] 127
rigid atoms, others: [1, 37, 38, 10, 11, 12, 13, 21, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 166
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071230 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2CC2(C)C)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 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, 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, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [33, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 57, 57, 57, 83, 83, 127, 127, 127, 127, 127, 57, 33, 33, 33, 1, 57, 57, 57, 127, 127, 127, 127, 127, 127, 127, 127, 57, 57] 127
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 407
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071230 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2CC2(C)C)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 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, 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, 7, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [57, 24, 57, 102, 102, 127, 127, 127, 127, 127, 24, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 57, 57, 57, 127, 24, 24, 24, 1, 1, 2, 2, 2, 2, 2, 2, 24, 24] 127
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 332
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071230 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071230
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071230/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071230
Building REAL250005071231
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071231'
/scratch/stefan/7916153/working/building/REAL250005071231 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071231

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071231/0 /scratch/stefan/7916153/working/building/REAL250005071231 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 353)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/353
`/scratch/stefan/7916153/working/3D/353' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2CCCO2)C1)

`REAL250005071231.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071231.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071231/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071231 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2CCCO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 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, 3, 7, 3, 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]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 21, 21, 54, 54, 54, 54, 54, 1, 1, 1, 1, 6, 6, 31, 31, 31, 31, 31, 1, 8, 8, 8, 54, 1, 1, 1, 31, 31, 31, 31, 31, 31, 1, 1] 151
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 21, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 173
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071231 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2CCCO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 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, 3, 7, 3, 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]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 54, 54, 54, 79, 79, 151, 151, 151, 151, 151, 54, 34, 34, 34, 1, 54, 54, 54, 151, 151, 151, 151, 151, 151, 54, 54] 151
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 451
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071231 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2CCCO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 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, 3, 7, 3, 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]
0  hydrogens need rotated
151  conformations in input
total number of sets (complete confs): 151
using faster count positions algorithm for large data
unique positions, atoms: [83, 31, 83, 131, 131, 151, 151, 151, 151, 151, 31, 31, 11, 1, 11, 1, 1, 1, 1, 1, 1, 31, 83, 83, 83, 151, 31, 31, 31, 1, 1, 1, 1, 1, 1, 31, 31] 151
rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36])
total number of confs: 388
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071231 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071231
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071231/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071231
Building REAL250005071232
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071232'
/scratch/stefan/7916153/working/building/REAL250005071232 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071232

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071232/0 /scratch/stefan/7916153/working/building/REAL250005071232 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 354)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/354
`/scratch/stefan/7916153/working/3D/354' -> `0.mol2'
Preparing input files

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

`REAL250005071232.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071232.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071232/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071232 none CCC(C)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 194, 159, 194, 51, 37, 51, 37, 37, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 37, 201, 201, 201, 201, 201, 194, 194, 194, 194, 159, 159, 37, 37, 37, 14, 14, 14, 1, 37, 37] 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: 836
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071232 none CCC(C)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 57, 24, 56, 5, 1, 5, 1, 1, 1, 1, 7, 7, 20, 20, 37, 37, 37, 37, 37, 1, 79, 79, 79, 79, 79, 57, 57, 57, 57, 24, 24, 1, 1, 1, 7, 7, 7, 37, 1, 1] 201
rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 39, 40, 20] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 431
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071232 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071232
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071232/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071232
Building REAL250005071233
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071233'
/scratch/stefan/7916153/working/building/REAL250005071233 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071233

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071233/0 /scratch/stefan/7916153/working/building/REAL250005071233 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 355)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/355
`/scratch/stefan/7916153/working/3D/355' -> `0.mol2'
Preparing input files

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

`REAL250005071233.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071233.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071233/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071233 none C#CCCCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 135, 123, 41, 35, 41, 35, 35, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 35, 201, 195, 196, 147, 147, 123, 123, 35, 35, 35, 14, 14, 14, 1, 35, 35] 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: 929
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071233 none C#CCCCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 16, 2, 1, 2, 1, 1, 1, 1, 7, 7, 20, 20, 35, 35, 35, 35, 35, 1, 46, 43, 43, 27, 27, 16, 16, 1, 1, 1, 7, 7, 7, 35, 1, 1] 201
rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 313
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071233 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071233
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071233/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071233
Building REAL250005071234
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071234'
/scratch/stefan/7916153/working/building/REAL250005071234 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071234

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071234/0 /scratch/stefan/7916153/working/building/REAL250005071234 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 356)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/356
`/scratch/stefan/7916153/working/3D/356' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC(C)(C)O)C1)

`REAL250005071234.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071234.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071234/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071234 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC(C)(C)O)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 25, 25, 68, 68, 68, 68, 68, 1, 1, 1, 1, 7, 7, 21, 38, 39, 39, 1, 9, 9, 9, 68, 1, 1, 1, 21, 21, 39, 39, 39, 39, 39, 39, 117, 1, 1] 603
rigid atoms, others: [1, 37, 38, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 395
number of broken/clashed sets: 76
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071234 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC(C)(C)O)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens 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, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 68, 68, 68, 93, 93, 182, 200, 201, 201, 68, 33, 33, 33, 1, 68, 68, 68, 182, 182, 201, 201, 201, 201, 201, 201, 603, 68, 68] 603
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 1374
number of broken/clashed sets: 76
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071234 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071234
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071234/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071234
Building REAL250005071235
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071235'
/scratch/stefan/7916153/working/building/REAL250005071235 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071235

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071235/0 /scratch/stefan/7916153/working/building/REAL250005071235 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 357)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/357
`/scratch/stefan/7916153/working/3D/357' -> `0.mol2'
Preparing input files

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

`REAL250005071235.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071235.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071235/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071235 none CC(C)[C@@H](O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens 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, 178, 197, 82, 178, 178, 57, 82, 57, 57, 23, 9, 23, 1, 9, 1, 1, 1, 1, 1, 1, 57, 201, 201, 201, 201, 201, 201, 201, 534, 57, 57, 57, 23, 23, 23, 1, 57, 57] 603
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: 1394
number of broken/clashed sets: 75
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071235 none CC(C)[C@@H](O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [58, 31, 56, 6, 31, 31, 1, 6, 1, 1, 1, 1, 9, 9, 29, 29, 57, 57, 57, 57, 57, 1, 59, 59, 59, 59, 59, 59, 59, 93, 1, 1, 1, 9, 9, 9, 57, 1, 1] 603
rigid atoms, others: [32, 37, 6, 8, 9, 10, 11, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 464
number of broken/clashed sets: 75
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071235 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071235
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071235/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071235
Building REAL250005071236
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071236'
/scratch/stefan/7916153/working/building/REAL250005071236 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071236

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071236/0 /scratch/stefan/7916153/working/building/REAL250005071236 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 358)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/358
`/scratch/stefan/7916153/working/3D/358' -> `0.mol2'
Preparing input files

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

`REAL250005071236.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071236.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071236/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071236 none CCC(C)=CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 126, 126, 126, 78, 58, 78, 58, 58, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 126, 126, 126, 126, 58, 58, 58, 19, 19, 19, 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: 861
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071236 none CCC(C)=CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 12, 12, 12, 4, 1, 4, 1, 1, 1, 1, 10, 10, 37, 37, 58, 58, 58, 58, 58, 1, 23, 23, 23, 23, 23, 12, 12, 12, 12, 1, 1, 1, 10, 10, 10, 58, 1, 1] 201
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 220
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071236 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071236
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071236/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071236
Building REAL250005071237
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071237'
/scratch/stefan/7916153/working/building/REAL250005071237 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071237

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071237/0 /scratch/stefan/7916153/working/building/REAL250005071237 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 359)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/359
`/scratch/stefan/7916153/working/3D/359' -> `0.mol2'
Preparing input files

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

`REAL250005071237.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071237.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071237/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071237 none CC(C)C#CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 88, 88, 70, 88, 70, 70, 30, 10, 30, 1, 10, 1, 1, 1, 1, 1, 1, 70, 88, 88, 88, 88, 88, 88, 88, 70, 70, 70, 30, 30, 30, 1, 70, 70] 88
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: 269
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071237 none CC(C)C#CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 11, 11, 38, 38, 70, 70, 70, 70, 70, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 11, 11, 11, 70, 1, 1] 88
rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 157
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071237 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071237
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071237/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071237
Building REAL250005071238
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071238'
/scratch/stefan/7916153/working/building/REAL250005071238 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071238

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071238/0 /scratch/stefan/7916153/working/building/REAL250005071238 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 360)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/360
`/scratch/stefan/7916153/working/3D/360' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C#CC2CC2)C1)

`REAL250005071238.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071238.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071238/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071238 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C#CC2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.1', 'C.1', '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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 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, 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]
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: [9, 1, 9, 23, 23, 43, 43, 43, 43, 43, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 9, 9, 9, 43, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1] 68
rigid atoms, others: [1, 34, 33, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32])
total number of confs: 101
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071238 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C#CC2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.1', 'C.1', '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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 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, 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]
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: [28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 43, 43, 43, 68, 68, 68, 68, 68, 68, 43, 28, 28, 28, 1, 43, 43, 43, 68, 68, 68, 68, 68, 43, 43] 68
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 211
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071238 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C#CC2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.1', 'C.1', '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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 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, 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]
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: [29, 6, 29, 58, 58, 68, 68, 68, 68, 68, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 29, 29, 68, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7] 68
rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34])
total number of confs: 170
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071238 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071238
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071238/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071238
Building REAL250005071239
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071239'
/scratch/stefan/7916153/working/building/REAL250005071239 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071239

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071239/0 /scratch/stefan/7916153/working/building/REAL250005071239 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 361)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/361
`/scratch/stefan/7916153/working/3D/361' -> `0.mol2'
Preparing input files

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

`REAL250005071239.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071239.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071239/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071239 none C=C(C)CCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 194, 66, 49, 66, 49, 49, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 49, 201, 201, 201, 201, 201, 201, 201, 194, 194, 49, 49, 49, 21, 21, 21, 1, 49, 49] 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: 786
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071239 none C=C(C)CCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 32, 70, 18, 4, 1, 4, 1, 1, 1, 1, 9, 9, 30, 30, 49, 49, 49, 49, 49, 1, 70, 70, 70, 70, 70, 32, 32, 18, 18, 1, 1, 1, 9, 9, 9, 49, 1, 1] 201
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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/7916153/working/building/REAL250005071239 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071239
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071239/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071239
Building REAL250005071240
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071240'
/scratch/stefan/7916153/working/building/REAL250005071240 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071240

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071240/0 /scratch/stefan/7916153/working/building/REAL250005071240 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 362)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/362
`/scratch/stefan/7916153/working/3D/362' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)CC2)C1)

`REAL250005071240.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071240.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071240/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071240 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 22, 22, 40, 40, 40, 40, 40, 1, 1, 1, 1, 7, 7, 14, 14, 14, 1, 9, 9, 9, 40, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 1, 1] 96
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 19, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 127
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071240 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 40, 40, 40, 56, 56, 96, 96, 96, 40, 25, 25, 25, 1, 40, 40, 40, 96, 96, 96, 96, 96, 96, 96, 40, 40] 96
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 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: 329
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071240 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [39, 14, 39, 71, 71, 96, 96, 96, 96, 96, 14, 14, 5, 1, 5, 1, 1, 1, 1, 14, 39, 39, 39, 96, 14, 14, 14, 2, 2, 2, 1, 1, 1, 1, 14, 14] 96
rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 231
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071240 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071240
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071240/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071240
Building REAL250005071241
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071241'
/scratch/stefan/7916153/working/building/REAL250005071241 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071241

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071241/0 /scratch/stefan/7916153/working/building/REAL250005071241 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 363)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/363
`/scratch/stefan/7916153/working/3D/363' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2CCCO2)C1)

`REAL250005071241.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071241.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071241/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071241 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2CCCO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 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, 3, 7, 3, 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]
0  hydrogens 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, 32, 32, 72, 72, 72, 72, 72, 1, 1, 1, 1, 6, 6, 34, 34, 34, 34, 34, 1, 9, 9, 9, 72, 1, 1, 1, 34, 34, 34, 34, 34, 34, 1, 1] 201
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 21, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34])
total number of confs: 214
number of broken/clashed sets: 108
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071241 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2CCCO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 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, 3, 7, 3, 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]
0  hydrogens 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, 10, 1, 10, 1, 1, 1, 1, 1, 1, 35, 72, 72, 72, 103, 103, 201, 201, 201, 201, 201, 72, 35, 35, 35, 1, 72, 72, 72, 201, 201, 201, 201, 201, 201, 72, 72] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 607
number of broken/clashed sets: 108
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071241 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2CCCO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 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, 3, 7, 3, 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]
0  hydrogens 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, 34, 107, 186, 186, 201, 201, 201, 201, 201, 34, 34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 107, 107, 107, 201, 34, 34, 34, 1, 1, 1, 1, 1, 1, 34, 34] 201
rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36])
total number of confs: 530
number of broken/clashed sets: 108
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071241 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071241
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071241/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071241
Building REAL250005071242
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071242'
/scratch/stefan/7916153/working/building/REAL250005071242 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071242

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071242/0 /scratch/stefan/7916153/working/building/REAL250005071242 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 364)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/364
`/scratch/stefan/7916153/working/3D/364' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NNN=C2)C1)

`REAL250005071242.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071242.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071242/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071242 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NNN=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 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]
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: [9, 1, 9, 21, 21, 35, 35, 35, 35, 35, 1, 1, 1, 1, 5, 5, 14, 14, 14, 14, 1, 9, 9, 9, 35, 1, 1, 1, 14, 14, 1, 1] 65
rigid atoms, others: [1, 10, 11, 12, 13, 20, 25, 26, 27, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29])
total number of confs: 98
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071242 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NNN=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 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]
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: [21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 35, 35, 35, 48, 48, 65, 65, 65, 65, 35, 21, 21, 21, 1, 35, 35, 35, 65, 65, 35, 35] 65
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 182
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071242 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NNN=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 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]
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: [36, 15, 36, 56, 56, 65, 65, 65, 65, 65, 15, 14, 7, 1, 7, 1, 1, 1, 1, 1, 15, 36, 36, 36, 65, 15, 14, 14, 1, 1, 15, 15] 65
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 169
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071242 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071242
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071242/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071242
Building REAL250005071243
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071243'
/scratch/stefan/7916153/working/building/REAL250005071243 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071243

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071243/0 /scratch/stefan/7916153/working/building/REAL250005071243 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 365)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/365
`/scratch/stefan/7916153/working/3D/365' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2(C)CC2)C1)

`REAL250005071243.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071243.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071243/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071243 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2(C)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 18, 18, 45, 45, 45, 45, 45, 1, 1, 1, 1, 4, 4, 19, 46, 46, 46, 1, 6, 6, 6, 45, 1, 1, 1, 19, 19, 46, 46, 46, 46, 46, 46, 46, 1, 1] 201
rigid atoms, others: [1, 37, 38, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 223
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071243 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2(C)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 45, 45, 45, 69, 69, 177, 201, 201, 201, 45, 25, 25, 25, 1, 45, 45, 45, 177, 177, 201, 201, 201, 201, 201, 201, 201, 45, 45] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 781
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071243 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2(C)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7, 7]
0  hydrogens 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, 46, 120, 179, 179, 201, 201, 201, 201, 201, 46, 46, 25, 8, 25, 1, 1, 1, 1, 1, 46, 120, 120, 120, 201, 44, 46, 46, 8, 8, 2, 2, 2, 1, 1, 1, 1, 46, 46] 201
rigid atoms, others: [33, 34, 35, 36, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 581
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071243 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071243
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071243/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071243
Building REAL250005071244
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071244'
/scratch/stefan/7916153/working/building/REAL250005071244 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071244

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071244/0 /scratch/stefan/7916153/working/building/REAL250005071244 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 366)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/366
`/scratch/stefan/7916153/working/3D/366' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CN=CO2)C1)

`REAL250005071244.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071244.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071244/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071244 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CN=CO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [9, 1, 9, 21, 21, 42, 42, 42, 42, 42, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 1, 9, 9, 9, 42, 1, 1, 1, 18, 17, 1, 1] 76
rigid atoms, others: [1, 10, 11, 12, 13, 20, 25, 26, 27, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29])
total number of confs: 114
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071244 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CN=CO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 42, 42, 42, 58, 58, 76, 76, 76, 76, 42, 26, 26, 26, 1, 42, 42, 42, 76, 76, 42, 42] 76
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 212
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071244 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CN=CO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [42, 18, 42, 64, 64, 76, 76, 76, 76, 76, 18, 17, 9, 1, 9, 1, 1, 1, 1, 1, 18, 42, 42, 42, 76, 18, 17, 18, 1, 1, 18, 18] 76
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 196
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071244 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071244
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071244/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071244
Building REAL250005071245
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071245'
/scratch/stefan/7916153/working/building/REAL250005071245 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071245

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071245/0 /scratch/stefan/7916153/working/building/REAL250005071245 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 367)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/367
`/scratch/stefan/7916153/working/3D/367' -> `0.mol2'
Preparing input files

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

`REAL250005071245.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071245.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071245/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071245 none C=CC(C)(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 64, 85, 85, 50, 64, 50, 50, 25, 10, 25, 1, 10, 1, 1, 1, 1, 1, 1, 50, 85, 85, 85, 85, 85, 85, 85, 85, 85, 50, 50, 50, 25, 25, 25, 1, 50, 50] 85
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: 291
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071245 none C=CC(C)(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [24, 12, 7, 12, 12, 1, 7, 1, 1, 1, 1, 7, 7, 25, 25, 50, 50, 50, 50, 50, 1, 24, 24, 24, 12, 12, 12, 12, 12, 12, 1, 1, 1, 7, 7, 7, 50, 1, 1] 85
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 178
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071245 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071245
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071245/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071245
Building REAL250005071246
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071246'
/scratch/stefan/7916153/working/building/REAL250005071246 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071246

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071246/0 /scratch/stefan/7916153/working/building/REAL250005071246 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 368)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/368
`/scratch/stefan/7916153/working/3D/368' -> `0.mol2'
Preparing input files

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

`REAL250005071246.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071246.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071246/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071246 none C[C@@H]1C[C@H]1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 32, 6, 32, 1, 6, 1, 1, 1, 1, 7, 7, 34, 34, 75, 75, 75, 75, 75, 1, 32, 32, 32, 32, 32, 1, 1, 1, 7, 7, 7, 75, 1, 1] 171
rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 220
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071246 none C[C@@H]1C[C@H]1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 32, 32, 32, 85, 85, 161, 161, 171, 171, 171, 171, 171, 32, 2, 2, 2, 1, 1, 32, 32, 32, 85, 85, 85, 171, 32, 32] 171
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: 448
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071246 none C[C@@H]1C[C@H]1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [171, 171, 171, 171, 110, 171, 75, 110, 75, 75, 25, 9, 25, 1, 9, 1, 1, 1, 1, 1, 1, 75, 171, 171, 171, 171, 171, 75, 75, 75, 25, 25, 25, 1, 75, 75] 171
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: 541
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071246 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071246
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071246/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071246
Building REAL250005071247
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071247'
/scratch/stefan/7916153/working/building/REAL250005071247 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071247

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071247/0 /scratch/stefan/7916153/working/building/REAL250005071247 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 369)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/369
`/scratch/stefan/7916153/working/3D/369' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)CCC2)C1)

`REAL250005071247.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071247.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071247/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071247 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 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: [7, 1, 7, 18, 18, 34, 34, 34, 34, 34, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 1, 7, 7, 7, 34, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1] 80
rigid atoms, others: [1, 37, 38, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 116
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071247 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 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: [23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 34, 34, 34, 61, 61, 80, 80, 80, 80, 34, 23, 23, 23, 1, 34, 34, 34, 80, 80, 80, 80, 80, 80, 80, 80, 80, 34, 34] 80
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 261
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071247 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 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, 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: [37, 15, 37, 65, 65, 80, 80, 80, 80, 80, 15, 15, 5, 1, 5, 1, 1, 1, 1, 1, 15, 37, 37, 37, 80, 15, 15, 15, 2, 2, 2, 1, 1, 1, 1, 1, 1, 15, 15] 80
rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38])
total number of confs: 210
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071247 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071247
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071247/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071247
Building REAL250005071248
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071248'
/scratch/stefan/7916153/working/building/REAL250005071248 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071248

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071248/0 /scratch/stefan/7916153/working/building/REAL250005071248 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 370)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/370
`/scratch/stefan/7916153/working/3D/370' -> `0.mol2'
Preparing input files

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

`REAL250005071248.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071248.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071248/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071248 none CCC(F)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 189, 89, 189, 68, 89, 68, 68, 26, 10, 26, 1, 10, 1, 1, 1, 1, 1, 1, 68, 201, 201, 201, 201, 201, 189, 68, 68, 68, 26, 26, 26, 1, 68, 68] 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: 774
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071248 none CCC(F)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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: [37, 25, 6, 25, 1, 6, 1, 1, 1, 1, 11, 11, 32, 32, 68, 68, 68, 68, 68, 1, 43, 43, 43, 43, 43, 25, 1, 1, 1, 11, 11, 11, 68, 1, 1] 201
rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 19, 26, 27, 28] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32])
total number of confs: 340
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071248 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071248
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071248/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071248
Building REAL250005071249
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071249'
/scratch/stefan/7916153/working/building/REAL250005071249 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071249

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071249/0 /scratch/stefan/7916153/working/building/REAL250005071249 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 371)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/371
`/scratch/stefan/7916153/working/3D/371' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCCF)C1)

`REAL250005071249.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071249.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071249/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071249 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCCF)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 15, 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, 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]
0  hydrogens 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, 19, 19, 44, 44, 44, 44, 44, 1, 1, 1, 1, 4, 4, 18, 25, 57, 1, 9, 9, 9, 44, 1, 1, 1, 18, 18, 31, 31, 51, 53, 1, 1] 201
rigid atoms, others: [1, 34, 33, 10, 11, 12, 13, 19, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32])
total number of confs: 355
number of broken/clashed sets: 121
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071249 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCCF)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 15, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 44, 44, 44, 59, 59, 177, 197, 201, 44, 20, 20, 20, 1, 44, 44, 44, 177, 177, 201, 201, 201, 201, 44, 44] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 828
number of broken/clashed sets: 121
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071249 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071249
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071249/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071249
Building REAL250005071250
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071250'
/scratch/stefan/7916153/working/building/REAL250005071250 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071250

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071250/0 /scratch/stefan/7916153/working/building/REAL250005071250 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 372)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/372
`/scratch/stefan/7916153/working/3D/372' -> `0.mol2'
Preparing input files

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

`REAL250005071250.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071250.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071250/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071250 none C[C@H]1C[C@@H]1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 25, 7, 25, 1, 7, 1, 1, 1, 1, 11, 11, 41, 41, 88, 88, 88, 88, 88, 1, 25, 25, 25, 25, 25, 1, 1, 1, 11, 11, 11, 88, 1, 1] 201
rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 230
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071250 none C[C@H]1C[C@@H]1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 9, 9, 25, 25, 25, 100, 100, 187, 187, 201, 201, 201, 201, 201, 25, 2, 2, 2, 1, 1, 25, 25, 25, 100, 100, 100, 201, 25, 25] 201
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: 528
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071250 none C[C@H]1C[C@@H]1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 88, 130, 88, 88, 31, 11, 31, 1, 11, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 201, 201, 88, 88, 88, 31, 31, 31, 1, 88, 88] 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: 651
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071250 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071250
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071250/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071250
Building REAL250005071251
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071251'
/scratch/stefan/7916153/working/building/REAL250005071251 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071251

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071251/0 /scratch/stefan/7916153/working/building/REAL250005071251 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 373)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/373
`/scratch/stefan/7916153/working/3D/373' -> `0.mol2'
Preparing input files

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

`REAL250005071251.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071251.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071251/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071251 none CC(C)C(F)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 5, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 77, 187, 58, 77, 58, 58, 22, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 201, 201, 187, 58, 58, 58, 22, 22, 22, 1, 58, 58] 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: 775
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071251 none CC(C)C(F)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 5, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 49, 6, 25, 1, 6, 1, 1, 1, 1, 9, 9, 30, 30, 58, 58, 58, 58, 58, 1, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 9, 9, 9, 58, 1, 1] 201
rigid atoms, others: [36, 5, 7, 8, 9, 10, 37, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35])
total number of confs: 326
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071251 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071251
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071251/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071251
Building REAL250005071252
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071252'
/scratch/stefan/7916153/working/building/REAL250005071252 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071252

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071252/0 /scratch/stefan/7916153/working/building/REAL250005071252 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 374)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/374
`/scratch/stefan/7916153/working/3D/374' -> `0.mol2'
Preparing input files

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

`REAL250005071252.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071252.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071252/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071252 none C=CCCCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [49, 49, 39, 34, 14, 11, 14, 11, 11, 7, 4, 7, 1, 4, 1, 1, 1, 1, 1, 1, 11, 49, 49, 49, 49, 49, 39, 39, 34, 34, 11, 11, 11, 7, 7, 7, 1, 11, 11] 49
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: 213
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071252 none C=CCCCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
49  conformations in input
total number of sets (complete confs): 49
using default count positions algorithm for smaller data
unique positions, atoms: [32, 27, 20, 14, 2, 1, 2, 1, 1, 1, 1, 7, 7, 9, 9, 11, 11, 11, 11, 11, 1, 32, 32, 32, 27, 27, 20, 20, 14, 14, 1, 1, 1, 7, 7, 7, 11, 1, 1] 49
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 168
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071252 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071252
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071252/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071252
Building REAL250005071253
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071253'
/scratch/stefan/7916153/working/building/REAL250005071253 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071253

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071253/0 /scratch/stefan/7916153/working/building/REAL250005071253 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 375)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/375
`/scratch/stefan/7916153/working/3D/375' -> `0.mol2'
Preparing input files

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

`REAL250005071253.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071253.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071253/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071253 none CCC(C)(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 108, 197, 197, 63, 108, 63, 63, 24, 9, 24, 1, 9, 1, 1, 1, 1, 1, 1, 63, 201, 201, 201, 201, 201, 197, 197, 197, 197, 197, 197, 63, 63, 63, 24, 24, 24, 1, 63, 63] 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: 798
number of broken/clashed sets: 201
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071253 none CCC(C)(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 19, 7, 19, 19, 1, 7, 1, 1, 1, 1, 11, 11, 36, 36, 63, 63, 63, 63, 63, 1, 33, 33, 33, 33, 33, 19, 19, 19, 19, 19, 19, 1, 1, 1, 11, 11, 11, 63, 1, 1] 201
rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 39, 40, 20] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 275
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071253 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071253
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071253/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071253
Building REAL250005071254
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071254'
/scratch/stefan/7916153/working/building/REAL250005071254 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071254

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071254/0 /scratch/stefan/7916153/working/building/REAL250005071254 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 376)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/376
`/scratch/stefan/7916153/working/3D/376' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(N)=O)C1)

`REAL250005071254.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071254.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071254/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071254 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(N)=O)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 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]
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: [7, 1, 7, 14, 14, 22, 22, 22, 22, 22, 1, 1, 1, 1, 3, 3, 12, 12, 1, 7, 7, 7, 22, 1, 1, 1, 11, 12, 1, 1] 48
rigid atoms, others: [1, 10, 11, 12, 13, 18, 23, 24, 25, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 19, 20, 21, 22, 26, 27])
total number of confs: 80
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071254 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(N)=O)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 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]
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: [18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 22, 22, 22, 25, 25, 48, 48, 22, 18, 18, 18, 1, 22, 22, 22, 48, 48, 22, 22] 48
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 22] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 155
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071254 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071254
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071254/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071254
Building REAL250005071255
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071255'
/scratch/stefan/7916153/working/building/REAL250005071255 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071255

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071255/0 /scratch/stefan/7916153/working/building/REAL250005071255 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 377)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/377
`/scratch/stefan/7916153/working/3D/377' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071255.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071255.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071255/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071255 none CC1CC1CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 34, 34, 15, 2, 1, 2, 1, 1, 1, 1, 8, 8, 23, 23, 46, 46, 46, 46, 46, 1, 34, 34, 34, 34, 34, 34, 34, 15, 15, 1, 1, 1, 8, 8, 8, 46, 1, 1] 164
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 207
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071255 none CC1CC1CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 23, 23, 34, 34, 34, 95, 95, 161, 161, 164, 164, 164, 164, 164, 34, 2, 2, 2, 1, 1, 1, 1, 6, 6, 34, 34, 34, 95, 95, 95, 164, 34, 34] 164
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: 499
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071255 none CC1CC1CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [164, 164, 164, 157, 66, 46, 66, 46, 46, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 46, 164, 164, 164, 164, 164, 164, 164, 157, 157, 46, 46, 46, 14, 14, 14, 1, 46, 46] 164
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: 606
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071255 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071255
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071255/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071255
Building REAL250005071256
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071256'
/scratch/stefan/7916153/working/building/REAL250005071256 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071256

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071256/0 /scratch/stefan/7916153/working/building/REAL250005071256 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 378)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/378
`/scratch/stefan/7916153/working/3D/378' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)CC1)

`REAL250005071256.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071256.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071256/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071256 none CCC1(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)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.3', '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, 1, 11, 8, 5, 5, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 15, 7, 1, 7, 1, 1, 1, 1, 10, 10, 39, 39, 67, 67, 67, 67, 67, 1, 15, 15, 22, 22, 22, 22, 22, 1, 1, 1, 11, 11, 11, 67, 1, 1, 15, 15, 15, 15] 174
rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 18, 26, 27, 28] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 226
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071256 none CCC1(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)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.3', '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, 1, 11, 8, 5, 5, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 5, 5, 15, 15, 15, 68, 68, 140, 140, 164, 164, 164, 164, 164, 15, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 68, 68, 68, 164, 15, 15, 1, 1, 1, 1] 174
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: 423
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071256 none CCC1(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)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.3', '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, 1, 11, 8, 5, 5, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 164, 103, 67, 103, 67, 67, 27, 11, 27, 1, 11, 1, 1, 1, 1, 1, 1, 67, 164, 164, 174, 174, 174, 174, 174, 67, 67, 67, 27, 27, 27, 1, 67, 67, 164, 164, 164, 164] 174
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: 575
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071256 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071256
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071256/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071256
Building REAL250005071257
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071257'
/scratch/stefan/7916153/working/building/REAL250005071257 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071257

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071257/0 /scratch/stefan/7916153/working/building/REAL250005071257 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 379)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/379
`/scratch/stefan/7916153/working/3D/379' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(CF)CC2)C1)

`REAL250005071257.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071257.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071257/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071257 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(CF)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 15, 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, 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
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 25, 25, 64, 64, 64, 64, 64, 1, 1, 1, 1, 6, 6, 13, 43, 13, 13, 1, 9, 9, 9, 64, 1, 1, 1, 43, 43, 13, 13, 13, 13, 1, 1] 182
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33])
total number of confs: 267
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071257 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(CF)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 15, 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, 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
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 64, 64, 64, 110, 110, 175, 182, 175, 175, 64, 28, 28, 28, 1, 64, 64, 64, 182, 182, 175, 175, 175, 175, 64, 64] 182
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 625
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071257 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(CF)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 15, 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, 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
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [48, 13, 48, 98, 98, 175, 175, 175, 175, 175, 13, 13, 5, 1, 5, 1, 1, 10, 1, 1, 13, 48, 48, 48, 175, 13, 13, 13, 10, 10, 1, 1, 1, 1, 13, 13] 182
rigid atoms, others: [32, 33, 13, 15, 16, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 399
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071257 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071257
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071257/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071257
Building REAL250005071258
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071258'
/scratch/stefan/7916153/working/building/REAL250005071258 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071258

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071258/0 /scratch/stefan/7916153/working/building/REAL250005071258 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 380)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/380
`/scratch/stefan/7916153/working/3D/380' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)C)C1)

`REAL250005071258.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071258.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071258/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071258 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)C)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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, 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, 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: [9, 1, 9, 29, 29, 65, 65, 65, 65, 65, 1, 1, 1, 1, 7, 7, 9, 9, 9, 1, 9, 9, 9, 65, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1] 85
rigid atoms, others: [1, 36, 37, 10, 11, 12, 13, 19, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 151
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071258 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)C)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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, 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, 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: [36, 10, 1, 10, 1, 1, 1, 1, 1, 1, 36, 65, 65, 65, 85, 85, 85, 85, 85, 65, 36, 36, 36, 1, 65, 65, 65, 85, 85, 85, 85, 85, 85, 85, 85, 85, 65, 65] 85
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 263
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071258 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071258
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071258/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071258
Building REAL250005071259
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071259'
/scratch/stefan/7916153/working/building/REAL250005071259 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071259

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071259/0 /scratch/stefan/7916153/working/building/REAL250005071259 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 381)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/381
`/scratch/stefan/7916153/working/3D/381' -> `0.mol2'
Preparing input files

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

`REAL250005071259.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071259.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071259/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071259 none CC(C)C(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 108, 110, 77, 108, 51, 77, 51, 51, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 51, 111, 111, 111, 111, 111, 111, 111, 108, 108, 108, 108, 51, 51, 51, 20, 20, 20, 1, 51, 51] 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: 405
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071259 none CC(C)C(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 21, 31, 6, 21, 1, 6, 1, 1, 1, 1, 7, 7, 31, 31, 51, 51, 51, 51, 51, 1, 32, 32, 32, 32, 32, 32, 32, 21, 22, 22, 22, 1, 1, 1, 7, 7, 7, 51, 1, 1] 111
rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 39, 40, 20] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 254
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071259 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071259
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071259/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071259
Building REAL250005071260
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071260'
/scratch/stefan/7916153/working/building/REAL250005071260 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071260

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071260/0 /scratch/stefan/7916153/working/building/REAL250005071260 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 382)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/382
`/scratch/stefan/7916153/working/3D/382' -> `0.mol2'
Preparing input files

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

`REAL250005071260.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071260.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071260/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071260 none CC[C@@H]1C[C@H]1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 28, 28, 28, 28, 6, 28, 1, 6, 1, 1, 1, 1, 7, 7, 27, 27, 49, 49, 49, 49, 49, 1, 45, 45, 45, 45, 45, 28, 28, 1, 1, 1, 7, 7, 7, 49, 1, 1] 201
rigid atoms, others: [32, 37, 38, 7, 9, 10, 11, 12, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 270
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071260 none CC[C@@H]1C[C@H]1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 28, 28, 28, 73, 73, 139, 139, 166, 166, 166, 166, 166, 28, 3, 3, 3, 3, 3, 1, 1, 28, 28, 28, 73, 73, 73, 166, 28, 28] 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: 429
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071260 none CC[C@@H]1C[C@H]1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 166, 166, 166, 166, 72, 166, 49, 72, 49, 49, 18, 8, 18, 1, 8, 1, 1, 1, 1, 1, 1, 49, 201, 201, 201, 201, 201, 166, 166, 49, 49, 49, 18, 18, 18, 1, 49, 49] 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: 703
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071260 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071260
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071260/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071260
Building REAL250005071261
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071261'
/scratch/stefan/7916153/working/building/REAL250005071261 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071261

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071261/0 /scratch/stefan/7916153/working/building/REAL250005071261 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 383)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/383
`/scratch/stefan/7916153/working/3D/383' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC23CC3)C1)

`REAL250005071261.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071261.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071261/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071261 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC23CC3)C1 NO_LONG_NAME
dock atom types: ['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.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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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: [7, 7, 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, 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: [8, 1, 8, 25, 25, 71, 71, 71, 71, 71, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 1, 9, 9, 9, 71, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 1, 1] 195
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 198
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071261 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC23CC3)C1 NO_LONG_NAME
dock atom types: ['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.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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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: [7, 7, 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, 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: [34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 71, 71, 71, 103, 103, 195, 195, 195, 195, 71, 34, 34, 34, 1, 71, 71, 71, 195, 195, 195, 195, 195, 195, 195, 71, 71] 195
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 613
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071261 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC23CC3)C1 NO_LONG_NAME
dock atom types: ['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.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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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: [7, 7, 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, 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: [93, 28, 93, 163, 163, 195, 195, 195, 195, 195, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 28, 93, 93, 93, 195, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 28, 28] 195
rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36])
total number of confs: 491
number of broken/clashed sets: 38
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071261 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071261
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071261/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071261
Building REAL250005071262
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071262'
/scratch/stefan/7916153/working/building/REAL250005071262 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071262

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071262/0 /scratch/stefan/7916153/working/building/REAL250005071262 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 384)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/384
`/scratch/stefan/7916153/working/3D/384' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2CC(=O)N2)C1)

`REAL250005071262.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071262.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071262/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071262 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2CC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 32, 32, 85, 85, 85, 85, 85, 1, 1, 1, 1, 6, 6, 34, 34, 34, 34, 34, 1, 10, 10, 10, 85, 1, 1, 1, 34, 34, 34, 1, 1] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 21, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 230
number of broken/clashed sets: 84
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071262 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2CC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 10, 1, 10, 1, 1, 1, 1, 1, 1, 38, 85, 85, 85, 110, 110, 201, 201, 201, 201, 201, 85, 38, 38, 38, 1, 85, 85, 85, 201, 201, 201, 85, 85] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 627
number of broken/clashed sets: 84
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071262 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2CC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [96, 34, 96, 180, 180, 201, 201, 201, 201, 201, 34, 34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 96, 96, 96, 201, 34, 34, 34, 1, 1, 1, 34, 34] 201
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 520
number of broken/clashed sets: 84
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071262 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071262
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071262/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071262
Building REAL250005071263
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071263'
/scratch/stefan/7916153/working/building/REAL250005071263 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071263

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071263/0 /scratch/stefan/7916153/working/building/REAL250005071263 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 385)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/385
`/scratch/stefan/7916153/working/3D/385' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2CC(=O)N2)C1)

`REAL250005071263.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071263.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071263/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071263 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2CC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 23, 23, 55, 55, 55, 55, 55, 1, 1, 1, 1, 6, 6, 31, 31, 31, 31, 31, 1, 9, 9, 9, 55, 1, 1, 1, 31, 31, 31, 1, 1] 168
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 21, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31])
total number of confs: 177
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071263 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2CC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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: [34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 55, 55, 55, 83, 83, 168, 168, 168, 168, 168, 55, 34, 34, 34, 1, 55, 55, 55, 168, 168, 168, 55, 55] 168
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 511
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071263 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2CC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 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: [91, 31, 91, 142, 142, 168, 168, 168, 168, 168, 31, 31, 11, 1, 11, 1, 1, 1, 1, 1, 1, 31, 91, 91, 91, 168, 31, 31, 31, 1, 1, 1, 31, 31] 168
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33])
total number of confs: 435
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071263 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071263
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071263/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071263
Building REAL250005071264
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071264'
/scratch/stefan/7916153/working/building/REAL250005071264 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071264

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071264/0 /scratch/stefan/7916153/working/building/REAL250005071264 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 386)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/386
`/scratch/stefan/7916153/working/3D/386' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)CC1)

`REAL250005071264.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071264.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071264/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071264 none COC1(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)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.3', '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, 12, 5, 1, 11, 8, 5, 5, 8, 5, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 7, 1, 7, 1, 1, 1, 1, 10, 10, 39, 39, 83, 83, 83, 83, 83, 1, 21, 21, 36, 36, 36, 1, 1, 1, 11, 11, 11, 83, 1, 1, 21, 21, 21, 21] 201
rigid atoms, others: [32, 3, 5, 6, 7, 8, 18, 24, 25, 26, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 27, 28, 29, 30, 33, 34, 35, 36])
total number of confs: 248
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071264 none COC1(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)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.3', '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, 12, 5, 1, 11, 8, 5, 5, 8, 5, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 9, 9, 22, 22, 22, 92, 92, 171, 171, 199, 199, 199, 199, 199, 22, 1, 1, 5, 5, 5, 22, 22, 22, 92, 92, 92, 199, 22, 22, 1, 1, 1, 1] 201
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: 504
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071264 none COC1(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)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.3', '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, 12, 5, 1, 11, 8, 5, 5, 8, 5, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 126, 83, 126, 83, 83, 30, 10, 30, 1, 10, 1, 1, 1, 1, 1, 1, 83, 199, 199, 201, 201, 201, 83, 83, 83, 30, 30, 30, 1, 83, 83, 199, 199, 199, 199] 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, 35, 36])
total number of confs: 655
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071264 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071264
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071264/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071264
Building REAL250005071265
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071265'
/scratch/stefan/7916153/working/building/REAL250005071265 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071265

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071265/0 /scratch/stefan/7916153/working/building/REAL250005071265 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 387)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/387
`/scratch/stefan/7916153/working/3D/387' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CSC2)C1)

`REAL250005071265.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071265.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071265/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071265 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CSC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 14, 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, 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
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, 37, 37, 106, 106, 106, 106, 106, 1, 1, 1, 1, 6, 6, 29, 29, 29, 1, 9, 9, 9, 106, 1, 1, 1, 29, 29, 29, 29, 29, 1, 1] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 19, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 252
number of broken/clashed sets: 113
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071265 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CSC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 14, 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, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 10, 1, 10, 1, 1, 1, 1, 1, 1, 39, 106, 106, 106, 166, 166, 201, 201, 201, 104, 39, 39, 39, 1, 106, 106, 106, 201, 201, 201, 201, 201, 106, 106] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 639
number of broken/clashed sets: 113
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071265 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CSC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 14, 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, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [111, 29, 111, 187, 187, 201, 201, 201, 201, 201, 29, 29, 8, 1, 8, 1, 1, 1, 1, 29, 111, 111, 111, 201, 29, 29, 29, 1, 1, 1, 1, 1, 29, 29] 201
rigid atoms, others: [13, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33])
total number of confs: 515
number of broken/clashed sets: 113
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071265 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071265
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071265/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071265
Building REAL250005071266
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071266'
/scratch/stefan/7916153/working/building/REAL250005071266 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071266

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071266/0 /scratch/stefan/7916153/working/building/REAL250005071266 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 388)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/388
`/scratch/stefan/7916153/working/3D/388' -> `0.mol2'
Preparing input files

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

`REAL250005071266.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071266.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071266/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071266 none C=CCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 100, 62, 100, 62, 62, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 62, 62, 62, 21, 21, 21, 1, 62, 62] 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])
total number of confs: 755
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071266 none C=CCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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: [62, 32, 6, 1, 6, 1, 1, 1, 1, 7, 7, 31, 31, 62, 62, 62, 62, 62, 1, 62, 62, 62, 32, 32, 1, 1, 1, 7, 7, 7, 62, 1, 1] 201
rigid atoms, others: [32, 3, 5, 6, 7, 8, 18, 24, 25, 26, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 329
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071266 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071266
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071266/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071266
Building REAL250005071267
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071267'
/scratch/stefan/7916153/working/building/REAL250005071267 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071267

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071267/0 /scratch/stefan/7916153/working/building/REAL250005071267 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 389)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/389
`/scratch/stefan/7916153/working/3D/389' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C[NH+](C)C)C1)

`REAL250005071267.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071267.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071267/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071267 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C[NH+](C)C)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 9, 6, 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, 3, 7, 3, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 8, 8, 15, 15, 15, 15, 15, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 1, 6, 6, 6, 15, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1] 31
rigid atoms, others: [1, 36, 37, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 97
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071267 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C[NH+](C)C)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 9, 6, 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, 3, 7, 3, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 15, 15, 15, 18, 18, 31, 31, 31, 31, 15, 14, 14, 14, 1, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15] 31
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 116
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071267 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071267/1 /scratch/stefan/7916153/working/building/REAL250005071267 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 390)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/390
`/scratch/stefan/7916153/working/3D/390' -> `1.mol2'
Preparing input files

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

`REAL250005071267.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071267.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071267/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071267 none CN(C)CC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 191, 201, 88, 65, 88, 65, 65, 23, 9, 23, 1, 9, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 201, 191, 191, 65, 65, 65, 23, 23, 23, 1, 65, 65] 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])
total number of confs: 761
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071267 none CN(C)CC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [44, 23, 44, 5, 1, 5, 1, 1, 1, 1, 11, 11, 36, 36, 65, 65, 65, 65, 65, 1, 44, 44, 44, 44, 44, 44, 23, 23, 1, 1, 1, 11, 11, 11, 65, 1, 1] 201
rigid atoms, others: [35, 4, 6, 7, 8, 9, 19, 36, 28, 29, 30] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 278
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071267 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071267
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071267/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071267/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071267
Building REAL250005071268
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071268'
/scratch/stefan/7916153/working/building/REAL250005071268 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071268

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071268/0 /scratch/stefan/7916153/working/building/REAL250005071268 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 391)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/391
`/scratch/stefan/7916153/working/3D/391' -> `0.mol2'
Preparing input files

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

`REAL250005071268.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071268.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071268/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071268 none C=CC(O)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
486  conformations in input
total number of sets (complete confs): 486
using faster count positions algorithm for large data
unique positions, atoms: [162, 162, 75, 162, 53, 75, 53, 53, 23, 8, 23, 1, 8, 1, 1, 1, 1, 1, 1, 53, 162, 162, 162, 162, 486, 53, 53, 53, 23, 23, 23, 1, 53, 53] 486
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: 1117
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071268 none C=CC(O)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
486  conformations in input
total number of sets (complete confs): 486
using faster count positions algorithm for large data
unique positions, atoms: [60, 31, 6, 31, 1, 6, 1, 1, 1, 1, 7, 7, 26, 26, 53, 53, 53, 53, 53, 1, 60, 60, 60, 31, 93, 1, 1, 1, 7, 7, 7, 53, 1, 1] 486
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 19, 25, 26, 27] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 398
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071268 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071268
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071268/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071268
Building REAL250005071269
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071269'
/scratch/stefan/7916153/working/building/REAL250005071269 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071269

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071269/0 /scratch/stefan/7916153/working/building/REAL250005071269 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 392)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/392
`/scratch/stefan/7916153/working/3D/392' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2COC2)C1)

`REAL250005071269.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071269.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071269/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071269 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2COC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 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, 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, 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: [7, 1, 7, 20, 20, 56, 56, 56, 56, 56, 1, 1, 1, 1, 6, 6, 24, 24, 24, 1, 7, 7, 7, 56, 1, 1, 1, 24, 24, 24, 24, 24, 1, 1] 128
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 19, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 160
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071269 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2COC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 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, 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, 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: [34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 56, 56, 56, 76, 76, 128, 128, 128, 56, 34, 34, 34, 1, 56, 56, 56, 128, 128, 128, 128, 128, 56, 56] 128
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 411
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071269 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2COC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 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, 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, 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: [73, 24, 73, 106, 106, 128, 128, 128, 128, 128, 24, 24, 8, 1, 8, 1, 1, 1, 1, 24, 73, 73, 73, 128, 24, 24, 24, 1, 1, 1, 1, 1, 24, 24] 128
rigid atoms, others: [13, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33])
total number of confs: 327
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071269 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071269
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071269/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071269
Building REAL250005071270
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071270'
/scratch/stefan/7916153/working/building/REAL250005071270 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071270

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071270/0 /scratch/stefan/7916153/working/building/REAL250005071270 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 393)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/393
`/scratch/stefan/7916153/working/3D/393' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CO[C@H](C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071270.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071270.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071270/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071270 none CO[C@H](C)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 167, 95, 167, 167, 67, 95, 67, 67, 26, 10, 26, 1, 10, 1, 1, 1, 1, 1, 1, 67, 171, 171, 171, 167, 167, 167, 67, 67, 67, 26, 26, 26, 1, 67, 67] 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: 637
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071270 none CO[C@H](C)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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: [54, 26, 7, 26, 26, 1, 6, 1, 1, 1, 1, 8, 8, 33, 33, 67, 67, 67, 67, 67, 1, 54, 54, 54, 26, 26, 26, 1, 1, 1, 9, 9, 9, 67, 1, 1] 171
rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 268
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071270 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071270
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071270/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071270
Building REAL250005071271
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071271'
/scratch/stefan/7916153/working/building/REAL250005071271 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071271

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071271/0 /scratch/stefan/7916153/working/building/REAL250005071271 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 394)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/394
`/scratch/stefan/7916153/working/3D/394' -> `0.mol2'
Preparing input files

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

`REAL250005071271.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071271.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071271/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071271 none CC=CC(O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 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, 173, 97, 173, 64, 97, 64, 64, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 64, 201, 201, 201, 201, 201, 173, 519, 64, 64, 64, 20, 20, 20, 1, 64, 64] 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: 1322
number of broken/clashed sets: 87
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071271 none CC=CC(O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 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: [37, 37, 14, 3, 14, 1, 3, 1, 1, 1, 1, 11, 11, 38, 38, 64, 64, 64, 64, 64, 1, 37, 37, 37, 37, 37, 14, 42, 1, 1, 1, 11, 11, 11, 64, 1, 1] 603
rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 288
number of broken/clashed sets: 87
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071271 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071271
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071271/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071271
Building REAL250005071272
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071272'
/scratch/stefan/7916153/working/building/REAL250005071272 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071272

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071272/0 /scratch/stefan/7916153/working/building/REAL250005071272 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 395)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/395
`/scratch/stefan/7916153/working/3D/395' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C)

`REAL250005071272.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071272.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071272/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071272 none C[C@@H](C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)[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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 7, 3, 7, 3, 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
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [12, 10, 12, 8, 10, 8, 8, 6, 4, 6, 1, 4, 1, 1, 1, 1, 1, 1, 8, 12, 12, 12, 12, 12, 12, 12, 8, 8, 8, 6, 6, 6, 1, 8, 8, 12, 12, 12, 12, 12, 12] 12
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, 39, 40])
total number of confs: 45
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071272 none C[C@@H](C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)[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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 7, 3, 7, 3, 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
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [8, 5, 8, 1, 5, 1, 1, 1, 1, 5, 5, 7, 7, 8, 8, 8, 8, 8, 1, 8, 9, 9, 9, 8, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 1, 9, 9, 9, 9, 9, 9] 12
rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 18, 26, 27, 28] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 50
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071272 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071272/1 /scratch/stefan/7916153/working/building/REAL250005071272 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 396)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/396
`/scratch/stefan/7916153/working/3D/396' -> `1.mol2'
Preparing input files

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

`REAL250005071272.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071272.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071272/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071272 none C[C@@H](C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [114, 63, 114, 45, 63, 45, 45, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 45, 114, 116, 116, 114, 114, 114, 45, 45, 45, 21, 21, 21, 1, 45, 45, 116, 116, 116, 116, 116, 116] 116
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, 39])
total number of confs: 449
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071272 none C[C@@H](C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [19, 5, 19, 1, 5, 1, 1, 1, 1, 9, 9, 27, 27, 45, 45, 45, 45, 45, 1, 19, 35, 35, 20, 20, 20, 1, 1, 1, 10, 10, 10, 45, 1, 1, 35, 35, 35, 35, 35, 35] 116
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 18, 25, 26, 27] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 226
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071272 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071272
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071272/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071272/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071272
Building REAL250005071273
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071273'
/scratch/stefan/7916153/working/building/REAL250005071273 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071273

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071273/0 /scratch/stefan/7916153/working/building/REAL250005071273 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 397)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/397
`/scratch/stefan/7916153/working/3D/397' -> `0.mol2'
Preparing input files

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

`REAL250005071273.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071273.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071273/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071273 none CCC=C(F)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 5, 1, 1, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 137, 137, 104, 137, 64, 104, 64, 64, 20, 9, 20, 1, 9, 1, 1, 1, 1, 1, 1, 64, 201, 201, 201, 201, 201, 137, 64, 64, 64, 20, 20, 20, 1, 64, 64] 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: 817
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071273 none CCC=C(F)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 5, 1, 1, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 17, 17, 7, 17, 1, 7, 1, 1, 1, 1, 11, 11, 41, 41, 64, 64, 64, 64, 64, 1, 36, 36, 36, 36, 36, 16, 1, 1, 1, 11, 11, 11, 64, 1, 1] 201
rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 270
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071273 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071273
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071273/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071273
Building REAL250005071274
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071274'
/scratch/stefan/7916153/working/building/REAL250005071274 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071274

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071274/0 /scratch/stefan/7916153/working/building/REAL250005071274 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 398)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/398
`/scratch/stefan/7916153/working/3D/398' -> `0.mol2'
Preparing input files

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

`REAL250005071274.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071274.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071274/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071274 none CCC=CC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 148, 148, 89, 61, 89, 61, 61, 21, 9, 21, 1, 9, 1, 1, 1, 1, 1, 1, 61, 201, 201, 201, 201, 201, 148, 148, 61, 61, 61, 21, 21, 21, 1, 61, 61] 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: 787
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071274 none CCC=CC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 18, 3, 1, 3, 1, 1, 1, 1, 11, 11, 39, 39, 61, 61, 61, 61, 61, 1, 35, 35, 35, 35, 35, 17, 18, 1, 1, 1, 11, 11, 11, 61, 1, 1] 201
rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 19, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 262
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071274 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071274
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071274/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071274
Building REAL250005071275
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071275'
/scratch/stefan/7916153/working/building/REAL250005071275 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL250005071275 as failed and skipping
/scratch/stefan/7916153/working /scratch/stefan/7916153
`/scratch/stefan/7916153/working/building/REAL250005071275' -> `/scratch/stefan/7916153/failed/REAL250005071275'
Building REAL250005071276
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071276'
/scratch/stefan/7916153/working/building/REAL250005071276 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071276

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071276/0 /scratch/stefan/7916153/working/building/REAL250005071276 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 399)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/399
`/scratch/stefan/7916153/working/3D/399' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)CO)C1)

`REAL250005071276.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071276.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071276/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071276 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)CO)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
471  conformations in input
total number of sets (complete confs): 471
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 22, 22, 56, 56, 56, 56, 56, 1, 1, 1, 1, 7, 7, 18, 18, 18, 44, 1, 9, 9, 9, 56, 1, 1, 1, 18, 18, 18, 18, 18, 18, 44, 44, 132, 1, 1] 471
rigid atoms, others: [1, 37, 38, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 408
number of broken/clashed sets: 459
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071276 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)CO)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
471  conformations in input
total number of sets (complete confs): 471
using faster count positions algorithm for large data
unique positions, atoms: [27, 8, 1, 8, 1, 1, 1, 1, 1, 1, 27, 56, 56, 56, 88, 88, 155, 155, 155, 157, 56, 27, 27, 27, 1, 56, 56, 56, 155, 155, 155, 155, 155, 155, 157, 157, 471, 56, 56] 471
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 1088
number of broken/clashed sets: 459
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071276 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071276
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071276/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071276
Building REAL250005071277
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071277'
/scratch/stefan/7916153/working/building/REAL250005071277 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071277

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071277/0 /scratch/stefan/7916153/working/building/REAL250005071277 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 400)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/400
`/scratch/stefan/7916153/working/3D/400' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(F)CCC2)C1)

`REAL250005071277.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071277.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071277/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071277 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(F)CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 21, 21, 48, 48, 48, 48, 48, 1, 1, 1, 1, 5, 5, 20, 20, 20, 20, 1, 9, 9, 9, 48, 1, 1, 1, 20, 20, 20, 20, 20, 20, 1, 1] 137
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33])
total number of confs: 145
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071277 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(F)CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 48, 48, 48, 67, 67, 137, 137, 137, 137, 48, 30, 30, 30, 1, 48, 48, 48, 137, 137, 137, 137, 137, 137, 48, 48] 137
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 423
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071277 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(F)CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [75, 20, 75, 120, 120, 137, 137, 137, 137, 137, 20, 20, 9, 1, 9, 1, 1, 1, 1, 1, 20, 75, 75, 75, 137, 20, 20, 20, 1, 1, 1, 1, 1, 1, 20, 20] 137
rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35])
total number of confs: 357
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071277 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071277
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071277/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071277
Building REAL250005071278
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071278'
/scratch/stefan/7916153/working/building/REAL250005071278 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071278

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071278/0 /scratch/stefan/7916153/working/building/REAL250005071278 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 401)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/401
`/scratch/stefan/7916153/working/3D/401' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CO)C1)

`REAL250005071278.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071278.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071278/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071278 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CO)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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]
1  hydrogens need rotated
480  conformations in input
total number of sets (complete confs): 480
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 35, 35, 95, 95, 95, 95, 95, 1, 1, 1, 1, 5, 5, 29, 1, 9, 9, 9, 95, 1, 1, 1, 29, 29, 87, 1, 1] 480
rigid atoms, others: [1, 10, 11, 12, 13, 17, 22, 23, 24, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 18, 19, 20, 21, 25, 26, 27])
total number of confs: 351
number of broken/clashed sets: 279
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071278 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CO)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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]
1  hydrogens need rotated
480  conformations in input
total number of sets (complete confs): 480
using faster count positions algorithm for large data
unique positions, atoms: [40, 10, 1, 10, 1, 1, 1, 1, 1, 1, 40, 95, 95, 95, 124, 124, 160, 93, 40, 40, 40, 1, 95, 95, 95, 160, 160, 480, 95, 95] 480
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 21] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 1067
number of broken/clashed sets: 279
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071278 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071278
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071278/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071278
Building REAL250005071279
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071279'
/scratch/stefan/7916153/working/building/REAL250005071279 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071279

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071279/0 /scratch/stefan/7916153/working/building/REAL250005071279 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 402)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/402
`/scratch/stefan/7916153/working/3D/402' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CC(N)=O)C1)

`REAL250005071279.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071279.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071279/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071279 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CC(N)=O)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 24, 57, 57, 57, 57, 57, 1, 1, 1, 1, 7, 7, 26, 26, 73, 73, 1, 9, 9, 9, 57, 1, 1, 1, 26, 25, 73, 73, 1, 1] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 297
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071279 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CC(N)=O)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 57, 57, 57, 91, 91, 164, 164, 201, 201, 57, 25, 25, 25, 1, 57, 57, 57, 164, 164, 201, 201, 57, 57] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 655
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071279 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071279
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071279/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071279
Building REAL250005071280
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071280'
/scratch/stefan/7916153/working/building/REAL250005071280 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071280

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071280/0 /scratch/stefan/7916153/working/building/REAL250005071280 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 403)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/403
`/scratch/stefan/7916153/working/3D/403' -> `0.mol2'
Preparing input files

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

`REAL250005071280.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071280.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071280/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071280 none CC(O)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
348  conformations in input
total number of sets (complete confs): 348
using faster count positions algorithm for large data
unique positions, atoms: [116, 66, 116, 54, 66, 54, 54, 24, 10, 24, 1, 10, 1, 1, 1, 1, 1, 1, 54, 116, 116, 116, 116, 348, 54, 54, 54, 24, 24, 24, 1, 54, 54] 348
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: 797
number of broken/clashed sets: 49
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071280 none CC(O)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
348  conformations in input
total number of sets (complete confs): 348
using faster count positions algorithm for large data
unique positions, atoms: [25, 7, 25, 1, 7, 1, 1, 1, 1, 8, 8, 30, 30, 54, 54, 54, 54, 54, 1, 25, 25, 25, 25, 75, 1, 1, 1, 8, 8, 8, 54, 1, 1] 348
rigid atoms, others: [32, 3, 5, 6, 7, 8, 18, 24, 25, 26, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 271
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071280 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071280
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071280/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071280
Building REAL250005071281
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071281'
/scratch/stefan/7916153/working/building/REAL250005071281 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071281

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071281/0 /scratch/stefan/7916153/working/building/REAL250005071281 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 404)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/404
`/scratch/stefan/7916153/working/3D/404' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(O)CCC2)C1)

`REAL250005071281.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071281.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071281/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071281 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(O)CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
357  conformations in input
total number of sets (complete confs): 357
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 22, 22, 47, 47, 47, 47, 47, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 1, 9, 9, 9, 47, 1, 1, 1, 66, 22, 22, 22, 22, 22, 22, 1, 1] 357
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 220
number of broken/clashed sets: 62
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071281 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(O)CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
357  conformations in input
total number of sets (complete confs): 357
using faster count positions algorithm for large data
unique positions, atoms: [27, 8, 1, 8, 1, 1, 1, 1, 1, 1, 27, 47, 47, 47, 68, 68, 119, 119, 119, 119, 47, 27, 27, 27, 1, 47, 47, 47, 357, 119, 119, 119, 119, 119, 119, 47, 47] 357
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 744
number of broken/clashed sets: 62
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071281 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(O)CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
357  conformations in input
total number of sets (complete confs): 357
using faster count positions algorithm for large data
unique positions, atoms: [67, 22, 67, 104, 104, 119, 119, 119, 119, 119, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 22, 67, 67, 67, 119, 22, 22, 22, 6, 1, 1, 1, 1, 1, 1, 22, 22] 357
rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36])
total number of confs: 318
number of broken/clashed sets: 62
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071281 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071281
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071281/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071281
Building REAL250005071282
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071282'
/scratch/stefan/7916153/working/building/REAL250005071282 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071282

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071282/0 /scratch/stefan/7916153/working/building/REAL250005071282 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 405)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/405
`/scratch/stefan/7916153/working/3D/405' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(O)C2CC2)C1)

`REAL250005071282.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071282.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071282/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071282 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(O)C2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
594  conformations in input
total number of sets (complete confs): 594
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 18, 18, 54, 54, 54, 54, 54, 1, 1, 1, 1, 6, 6, 31, 31, 62, 62, 1, 7, 7, 7, 54, 1, 1, 1, 31, 93, 62, 62, 62, 62, 62, 1, 1] 594
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 391
number of broken/clashed sets: 86
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071282 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(O)C2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
594  conformations in input
total number of sets (complete confs): 594
using faster count positions algorithm for large data
unique positions, atoms: [34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 54, 54, 54, 82, 82, 171, 171, 198, 198, 54, 34, 34, 34, 1, 54, 54, 54, 171, 513, 198, 198, 198, 198, 198, 54, 54] 594
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 1280
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071282 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(O)C2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
594  conformations in input
total number of sets (complete confs): 594
using faster count positions algorithm for large data
unique positions, atoms: [124, 62, 124, 179, 179, 198, 198, 198, 198, 198, 62, 62, 29, 7, 29, 1, 7, 1, 1, 1, 62, 124, 124, 124, 198, 62, 62, 62, 7, 21, 1, 1, 1, 1, 1, 62, 62] 594
rigid atoms, others: [32, 33, 34, 15, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36])
total number of confs: 538
number of broken/clashed sets: 86
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071282 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071282
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071282/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071282
Building REAL250005071283
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071283'
/scratch/stefan/7916153/working/building/REAL250005071283 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071283

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071283/0 /scratch/stefan/7916153/working/building/REAL250005071283 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 406)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/406
`/scratch/stefan/7916153/working/3D/406' -> `0.mol2'
Preparing input files

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

`REAL250005071283.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071283.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071283/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071283 none C=CCC(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 76, 154, 56, 76, 56, 56, 22, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 201, 201, 154, 154, 154, 154, 56, 56, 56, 22, 22, 22, 1, 56, 56] 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: 873
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071283 none C=CCC(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [65, 34, 14, 5, 14, 1, 5, 1, 1, 1, 1, 7, 7, 29, 29, 56, 56, 56, 56, 56, 1, 65, 65, 65, 34, 34, 14, 14, 14, 14, 1, 1, 1, 7, 7, 7, 56, 1, 1] 201
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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
/scratch/stefan/7916153/working/building/REAL250005071283 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071283
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071283/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071283
Building REAL250005071284
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071284'
/scratch/stefan/7916153/working/building/REAL250005071284 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071284

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071284/0 /scratch/stefan/7916153/working/building/REAL250005071284 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 407)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/407
`/scratch/stefan/7916153/working/3D/407' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2F)C1)

`REAL250005071284.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071284.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071284/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071284 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2F)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
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, 35, 35, 93, 93, 93, 93, 93, 1, 1, 1, 1, 6, 6, 31, 31, 31, 1, 9, 9, 9, 93, 1, 1, 1, 31, 31, 31, 31, 1, 1] 201
rigid atoms, others: [32, 1, 10, 11, 12, 13, 19, 24, 25, 26, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 238
number of broken/clashed sets: 105
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071284 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2F)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 10, 1, 10, 1, 1, 1, 1, 1, 1, 36, 93, 93, 93, 141, 141, 201, 201, 201, 92, 36, 36, 36, 1, 93, 93, 93, 201, 201, 201, 201, 93, 93] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 650
number of broken/clashed sets: 105
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071284 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC2F)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [102, 31, 102, 183, 183, 201, 201, 201, 201, 201, 31, 31, 9, 1, 9, 1, 1, 1, 1, 31, 102, 102, 102, 201, 31, 31, 31, 1, 1, 1, 1, 31, 31] 201
rigid atoms, others: [13, 15, 16, 17, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32])
total number of confs: 525
number of broken/clashed sets: 105
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071284 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071284
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071284/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071284
Building REAL250005071285
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071285'
/scratch/stefan/7916153/working/building/REAL250005071285 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071285

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071285/0 /scratch/stefan/7916153/working/building/REAL250005071285 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 408)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/408
`/scratch/stefan/7916153/working/3D/408' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C)

`REAL250005071285.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071285.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071285/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071285 none C[C@@H](C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)[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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 7, 3, 7, 3, 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
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [12, 10, 12, 8, 10, 8, 8, 6, 4, 6, 1, 4, 1, 1, 1, 1, 1, 1, 8, 12, 12, 12, 12, 12, 12, 12, 8, 8, 8, 6, 6, 6, 1, 8, 8, 12, 12, 12, 12, 12, 12] 12
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, 39, 40])
total number of confs: 45
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071285 none C[C@@H](C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)[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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 7, 3, 7, 3, 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
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [8, 5, 8, 1, 5, 1, 1, 1, 1, 5, 5, 7, 7, 8, 8, 8, 8, 8, 1, 8, 9, 9, 9, 8, 8, 8, 1, 1, 1, 5, 5, 5, 8, 1, 1, 9, 9, 9, 9, 9, 9] 12
rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 18, 26, 27, 28] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 50
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071285 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071285/1 /scratch/stefan/7916153/working/building/REAL250005071285 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 409)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/409
`/scratch/stefan/7916153/working/3D/409' -> `1.mol2'
Preparing input files

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

`REAL250005071285.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071285.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071285/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071285 none C[C@@H](C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [114, 63, 114, 45, 63, 45, 45, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 45, 114, 116, 116, 114, 114, 114, 45, 45, 45, 21, 21, 21, 1, 45, 45, 116, 116, 116, 116, 116, 116] 116
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, 39])
total number of confs: 449
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071285 none C[C@@H](C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [19, 5, 19, 1, 5, 1, 1, 1, 1, 9, 9, 27, 27, 45, 45, 45, 45, 45, 1, 19, 35, 35, 20, 20, 20, 1, 1, 1, 10, 10, 10, 45, 1, 1, 35, 35, 35, 35, 35, 35] 116
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 18, 25, 26, 27] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 226
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071285 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071285
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071285/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071285/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071285
Building REAL250005071286
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071286'
/scratch/stefan/7916153/working/building/REAL250005071286 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071286

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071286/0 /scratch/stefan/7916153/working/building/REAL250005071286 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 410)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/410
`/scratch/stefan/7916153/working/3D/410' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCF)C1)

`REAL250005071286.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071286.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071286/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071286 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCF)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens 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, 26, 26, 63, 63, 63, 63, 63, 1, 1, 1, 1, 3, 3, 17, 38, 1, 9, 9, 9, 63, 1, 1, 1, 17, 17, 38, 38, 1, 1] 201
rigid atoms, others: [1, 10, 11, 12, 13, 18, 23, 24, 25, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 19, 20, 21, 22, 26, 27, 28, 29])
total number of confs: 283
number of broken/clashed sets: 110
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071286 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCF)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 6, 1, 6, 1, 1, 1, 1, 1, 1, 26, 63, 63, 63, 88, 88, 190, 201, 63, 26, 26, 26, 1, 63, 63, 63, 190, 190, 201, 201, 63, 63] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 22] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 785
number of broken/clashed sets: 110
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071286 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071286
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071286/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071286
Building REAL250005071287
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071287'
/scratch/stefan/7916153/working/building/REAL250005071287 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071287

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071287/0 /scratch/stefan/7916153/working/building/REAL250005071287 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 411)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/411
`/scratch/stefan/7916153/working/3D/411' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(O)COC2)C1)

`REAL250005071287.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071287.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071287/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071287 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(O)COC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 12, 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, 3, 7, 3, 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]
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: [8, 1, 8, 21, 21, 44, 44, 44, 44, 44, 1, 1, 1, 1, 5, 5, 25, 25, 25, 25, 1, 9, 9, 9, 44, 1, 1, 1, 75, 25, 25, 25, 25, 1, 1] 345
rigid atoms, others: [1, 34, 33, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32])
total number of confs: 225
number of broken/clashed sets: 61
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071287 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(O)COC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 12, 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, 3, 7, 3, 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]
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: [25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 44, 44, 44, 66, 66, 115, 115, 115, 115, 44, 25, 25, 25, 1, 44, 44, 44, 345, 115, 115, 115, 115, 44, 44] 345
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 720
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071287 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(O)COC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 12, 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, 3, 7, 3, 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]
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: [66, 25, 66, 101, 101, 115, 115, 115, 115, 115, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 25, 66, 66, 66, 115, 25, 25, 25, 3, 1, 1, 1, 1, 25, 25] 345
rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34])
total number of confs: 294
number of broken/clashed sets: 61
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071287 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071287
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071287/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071287
Building REAL250005071288
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071288'
/scratch/stefan/7916153/working/building/REAL250005071288 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071288

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071288/0 /scratch/stefan/7916153/working/building/REAL250005071288 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 412)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/412
`/scratch/stefan/7916153/working/3D/412' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)=C1CC1)

`REAL250005071288.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071288.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071288/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071288 none CC(C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)=C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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, 107, 72, 107, 72, 72, 27, 10, 27, 1, 10, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 201, 72, 72, 72, 27, 27, 27, 1, 72, 72, 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])
total number of confs: 615
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071288 none CC(C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)=C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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: [25, 6, 1, 6, 1, 1, 1, 1, 10, 10, 36, 36, 72, 72, 72, 72, 72, 1, 25, 25, 25, 26, 26, 26, 1, 1, 1, 11, 11, 11, 72, 1, 1, 25, 25, 25, 25] 201
rigid atoms, others: [32, 2, 4, 5, 6, 7, 17, 24, 25, 26, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 33, 34, 35, 36])
total number of confs: 218
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071288 none CC(C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)=C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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, 9, 9, 25, 25, 25, 98, 98, 183, 183, 201, 201, 201, 201, 201, 25, 1, 1, 1, 2, 2, 2, 25, 25, 25, 98, 98, 98, 201, 25, 25, 1, 1, 1, 1] 201
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: 528
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071288 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071288
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071288/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071288
Building REAL250005071289
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071289'
/scratch/stefan/7916153/working/building/REAL250005071289 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071289

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071289/0 /scratch/stefan/7916153/working/building/REAL250005071289 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 413)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/413
`/scratch/stefan/7916153/working/3D/413' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1CC1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071289.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071289.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071289/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071289 none CCC1CC1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 9, 9, 32, 32, 56, 56, 56, 56, 56, 1, 34, 34, 34, 34, 34, 20, 20, 20, 20, 1, 1, 1, 9, 9, 9, 56, 1, 1] 201
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 248
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071289 none CCC1CC1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 78, 78, 151, 151, 171, 171, 171, 171, 171, 20, 3, 3, 3, 3, 3, 1, 1, 1, 1, 20, 20, 20, 78, 78, 78, 171, 20, 20] 201
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: 452
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071289 none CCC1CC1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 77, 56, 77, 56, 56, 21, 7, 21, 1, 7, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 201, 201, 171, 171, 171, 171, 56, 56, 56, 21, 21, 21, 1, 56, 56] 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: 703
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071289 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071289
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071289/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071289
Building REAL250005071290
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071290'
/scratch/stefan/7916153/working/building/REAL250005071290 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071290

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071290/0 /scratch/stefan/7916153/working/building/REAL250005071290 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 414)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/414
`/scratch/stefan/7916153/working/3D/414' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2(O)CC2)C1)

`REAL250005071290.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071290.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071290/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071290 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2(O)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 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, 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, 7, 7, 7]
1  hydrogens 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, 21, 21, 57, 57, 57, 57, 57, 1, 1, 1, 1, 6, 6, 24, 56, 56, 56, 1, 7, 7, 7, 57, 1, 1, 1, 24, 24, 168, 56, 56, 56, 56, 1, 1] 603
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 446
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071290 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2(O)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 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, 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, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 57, 57, 57, 88, 88, 179, 201, 201, 201, 57, 34, 34, 34, 1, 57, 57, 57, 179, 179, 603, 201, 201, 201, 201, 57, 57] 603
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 1347
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071290 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CC2(O)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 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, 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, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [121, 56, 121, 181, 181, 201, 201, 201, 201, 201, 56, 56, 28, 8, 28, 1, 1, 1, 1, 1, 56, 121, 121, 121, 201, 54, 56, 56, 8, 8, 6, 1, 1, 1, 1, 56, 56] 603
rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 559
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071290 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071290
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071290/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071290
Building REAL250005071291
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071291'
/scratch/stefan/7916153/working/building/REAL250005071291 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071291

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071291/0 /scratch/stefan/7916153/working/building/REAL250005071291 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 415)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/415
`/scratch/stefan/7916153/working/3D/415' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CCF)C1)

`REAL250005071291.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071291.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071291/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071291 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CCF)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
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, 24, 24, 65, 65, 65, 65, 65, 1, 1, 1, 1, 7, 7, 26, 26, 83, 1, 9, 9, 9, 65, 1, 1, 1, 26, 25, 83, 83, 1, 1] 201
rigid atoms, others: [32, 1, 10, 11, 12, 13, 19, 24, 25, 26, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 399
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071291 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CCF)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 65, 65, 65, 108, 108, 186, 186, 201, 65, 29, 29, 29, 1, 65, 65, 65, 186, 186, 201, 201, 65, 65] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 667
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071291 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071291
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071291/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071291
Building REAL250005071292
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071292'
/scratch/stefan/7916153/working/building/REAL250005071292 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071292

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071292/0 /scratch/stefan/7916153/working/building/REAL250005071292 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 416)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/416
`/scratch/stefan/7916153/working/3D/416' -> `0.mol2'
Preparing input files

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

`REAL250005071292.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071292.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071292/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071292 none C#CCCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 187, 73, 52, 73, 52, 52, 22, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 52, 201, 201, 201, 187, 187, 52, 52, 52, 22, 22, 22, 1, 52, 52] 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])
total number of confs: 789
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071292 none C#CCCC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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: [34, 34, 20, 6, 1, 6, 1, 1, 1, 1, 10, 10, 34, 34, 52, 52, 52, 52, 52, 1, 34, 34, 34, 20, 20, 1, 1, 1, 10, 10, 10, 52, 1, 1] 201
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 19, 25, 26, 27] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 253
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071292 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071292
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071292/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071292
Building REAL250005071293
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071293'
/scratch/stefan/7916153/working/building/REAL250005071293 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071293

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071293/0 /scratch/stefan/7916153/working/building/REAL250005071293 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 417)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/417
`/scratch/stefan/7916153/working/3D/417' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CN2CCC2)C1)

`REAL250005071293.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071293.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071293/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071293 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CN2CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 10, 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, 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, 7, 7]
0  hydrogens 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, 23, 23, 55, 55, 55, 55, 55, 1, 1, 1, 1, 7, 7, 34, 64, 64, 64, 1, 9, 9, 9, 55, 1, 1, 1, 34, 34, 64, 64, 64, 64, 64, 64, 1, 1] 201
rigid atoms, others: [1, 36, 37, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 267
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071293 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CN2CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 10, 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, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 8, 1, 8, 1, 1, 1, 1, 1, 1, 27, 55, 55, 55, 88, 88, 181, 201, 201, 201, 55, 27, 27, 27, 1, 55, 55, 55, 181, 181, 201, 201, 201, 201, 201, 201, 55, 55] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 727
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071293 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CN2CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 10, 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, 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, 7, 7]
0  hydrogens 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, 64, 136, 190, 190, 201, 201, 201, 201, 201, 64, 64, 34, 6, 34, 1, 1, 1, 1, 1, 64, 136, 136, 136, 201, 64, 64, 64, 6, 6, 1, 1, 1, 1, 1, 1, 64, 64] 201
rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37])
total number of confs: 549
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071293 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071293/1 /scratch/stefan/7916153/working/building/REAL250005071293 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 418)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/418
`/scratch/stefan/7916153/working/3D/418' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C[NH+]2CCC2)C1)

`REAL250005071293.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071293.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071293/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071293 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C[NH+]2CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 9, 6, 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, 3, 7, 3, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 1, 3, 3, 3, 8, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1] 12
rigid atoms, others: [1, 37, 38, 10, 11, 12, 13, 21, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 52
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071293 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C[NH+]2CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 9, 6, 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, 3, 7, 3, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 8, 8, 8, 8, 1, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8] 12
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 25] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 29
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071293 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C[NH+]2CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 9, 6, 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, 3, 7, 3, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 10, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 7, 5, 7, 1, 1, 1, 1, 1, 1, 10, 12, 12, 12, 12, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 10, 10] 12
rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38])
total number of confs: 38
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071293 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071293
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071293/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071293/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071293
Building REAL250005071294
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071294'
/scratch/stefan/7916153/working/building/REAL250005071294 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071294

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071294/0 /scratch/stefan/7916153/working/building/REAL250005071294 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 419)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/419
`/scratch/stefan/7916153/working/3D/419' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#C[C@H]1C[C@H]1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071294.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071294.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071294/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071294 none C#C[C@H]1C[C@H]1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
181  conformations in input
total number of sets (complete confs): 181
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 18, 18, 7, 18, 1, 7, 1, 1, 1, 1, 11, 11, 41, 41, 94, 94, 94, 94, 94, 1, 18, 18, 18, 1, 1, 1, 11, 11, 11, 94, 1, 1] 181
rigid atoms, others: [33, 34, 7, 9, 10, 11, 12, 22, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32])
total number of confs: 221
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071294 none C#C[C@H]1C[C@H]1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
181  conformations in input
total number of sets (complete confs): 181
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 72, 72, 147, 147, 181, 181, 181, 181, 181, 18, 1, 1, 1, 18, 18, 18, 72, 72, 72, 181, 18, 18] 181
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: 465
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071294 none C#C[C@H]1C[C@H]1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
181  conformations in input
total number of sets (complete confs): 181
using faster count positions algorithm for large data
unique positions, atoms: [181, 181, 181, 181, 181, 138, 181, 94, 138, 94, 94, 35, 12, 35, 1, 12, 1, 1, 1, 1, 1, 1, 94, 181, 181, 181, 94, 94, 94, 35, 35, 35, 1, 94, 94] 181
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, 33, 34])
total number of confs: 581
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071294 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071294
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071294/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071294
Building REAL250005071295
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071295'
/scratch/stefan/7916153/working/building/REAL250005071295 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071295

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071295/0 /scratch/stefan/7916153/working/building/REAL250005071295 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 420)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/420
`/scratch/stefan/7916153/working/3D/420' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2C3CCC32)C1)

`REAL250005071295.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071295.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071295/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071295 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2C3CCC32)C1 NO_LONG_NAME
dock atom types: ['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.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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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: [7, 7, 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, 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: [9, 1, 9, 25, 25, 55, 55, 55, 55, 55, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 1, 9, 9, 9, 55, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 1, 1] 164
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 158
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071295 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2C3CCC32)C1 NO_LONG_NAME
dock atom types: ['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.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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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: [7, 7, 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, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 55, 55, 55, 85, 85, 164, 164, 164, 164, 55, 28, 28, 28, 1, 55, 55, 55, 164, 164, 164, 164, 164, 164, 164, 55, 55] 164
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 527
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071295 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2C3CCC32)C1 NO_LONG_NAME
dock atom types: ['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.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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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: [7, 7, 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, 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: [78, 20, 78, 139, 139, 164, 164, 164, 164, 164, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 20, 78, 78, 78, 164, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 20, 20] 164
rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36])
total number of confs: 420
number of broken/clashed sets: 32
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071295 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071295
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071295/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071295
Building REAL250005071296
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071296'
/scratch/stefan/7916153/working/building/REAL250005071296 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071296

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071296/0 /scratch/stefan/7916153/working/building/REAL250005071296 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 421)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/421
`/scratch/stefan/7916153/working/3D/421' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CCC1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071296.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071296.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071296/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071296 none C=C1CCC1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 22, 5, 1, 5, 1, 1, 1, 1, 10, 10, 38, 38, 71, 71, 71, 71, 71, 1, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 11, 11, 11, 71, 1, 1] 184
rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 204
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071296 none C=C1CCC1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 22, 22, 22, 86, 86, 172, 172, 184, 184, 184, 184, 184, 22, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 86, 86, 86, 184, 22, 22] 184
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: 486
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071296 none C=C1CCC1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [184, 184, 184, 184, 96, 71, 96, 71, 71, 30, 10, 30, 1, 10, 1, 1, 1, 1, 1, 1, 71, 184, 184, 184, 184, 184, 184, 184, 71, 71, 71, 30, 30, 30, 1, 71, 71] 184
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: 573
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071296 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071296
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071296/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071296
Building REAL250005071297
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071297'
/scratch/stefan/7916153/working/building/REAL250005071297 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071297

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071297/0 /scratch/stefan/7916153/working/building/REAL250005071297 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 422)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/422
`/scratch/stefan/7916153/working/3D/422' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1C(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)[C@H]1C)

`REAL250005071297.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071297.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071297/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071297 none C[C@H]1C(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)[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.3', '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, 7, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 11, 11, 39, 39, 63, 63, 63, 63, 63, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 11, 11, 11, 63, 1, 1, 8, 8, 8] 103
rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 19, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 36, 37, 38])
total number of confs: 153
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071297 none C[C@H]1C(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)[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.3', '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, 7, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 47, 47, 94, 94, 103, 103, 103, 103, 103, 8, 1, 1, 1, 2, 2, 2, 1, 8, 8, 8, 47, 47, 47, 103, 8, 8, 2, 2, 2] 103
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: 290
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071297 none C[C@H]1C(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)[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.3', '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, 7, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 103, 63, 103, 63, 63, 26, 8, 26, 1, 8, 1, 1, 1, 1, 1, 1, 63, 103, 103, 103, 103, 103, 103, 103, 63, 63, 63, 26, 26, 26, 1, 63, 63, 103, 103, 103] 103
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: 295
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071297 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071297
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071297/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071297
Building REAL250005071298
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071298'
/scratch/stefan/7916153/working/building/REAL250005071298 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071298

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071298/0 /scratch/stefan/7916153/working/building/REAL250005071298 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 423)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/423
`/scratch/stefan/7916153/working/3D/423' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C)

`REAL250005071298.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071298.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071298/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071298 none C[C@H](C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)[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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 7, 3, 7, 3, 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
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [36, 22, 36, 18, 22, 18, 18, 14, 8, 14, 1, 8, 1, 1, 1, 1, 1, 1, 18, 36, 38, 38, 38, 36, 36, 36, 18, 18, 18, 14, 14, 14, 1, 18, 18, 38, 38, 38, 38, 38, 38] 38
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, 39, 40])
total number of confs: 149
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071298 none C[C@H](C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)[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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 7, 3, 7, 3, 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
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [15, 5, 15, 1, 5, 1, 1, 1, 1, 7, 7, 10, 10, 18, 18, 18, 18, 18, 1, 15, 22, 22, 22, 15, 15, 15, 1, 1, 1, 7, 7, 7, 18, 1, 1, 22, 22, 22, 22, 22, 22] 38
rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 18, 26, 27, 28] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 125
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071298 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071298/1 /scratch/stefan/7916153/working/building/REAL250005071298 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 424)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/424
`/scratch/stefan/7916153/working/3D/424' -> `1.mol2'
Preparing input files

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

`REAL250005071298.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071298.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071298/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071298 none C[C@H](C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [127, 71, 127, 56, 71, 56, 56, 23, 9, 23, 1, 9, 1, 1, 1, 1, 1, 1, 56, 127, 132, 132, 127, 127, 127, 56, 56, 56, 23, 23, 23, 1, 56, 56, 132, 132, 132, 132, 132, 132] 132
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, 39])
total number of confs: 492
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071298 none C[C@H](C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [17, 4, 17, 1, 4, 1, 1, 1, 1, 9, 9, 31, 31, 56, 56, 56, 56, 56, 1, 17, 35, 35, 17, 17, 17, 1, 1, 1, 10, 10, 10, 56, 1, 1, 35, 35, 35, 35, 35, 35] 132
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 18, 25, 26, 27] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 235
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071298 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071298
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071298/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071298/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071298
Building REAL250005071299
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071299'
/scratch/stefan/7916153/working/building/REAL250005071299 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071299

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071299/0 /scratch/stefan/7916153/working/building/REAL250005071299 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 425)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/425
`/scratch/stefan/7916153/working/3D/425' -> `0.mol2'
Preparing input files

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

`REAL250005071299.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071299.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071299/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071299 none CC=CC=CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 181, 111, 76, 111, 76, 76, 30, 10, 30, 1, 10, 1, 1, 1, 1, 1, 1, 76, 201, 201, 201, 201, 201, 181, 181, 76, 76, 76, 30, 30, 30, 1, 76, 76] 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: 641
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071299 none CC=CC=CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 23, 7, 1, 7, 1, 1, 1, 1, 11, 11, 39, 39, 76, 76, 76, 76, 76, 1, 35, 35, 35, 35, 35, 22, 23, 1, 1, 1, 11, 11, 11, 76, 1, 1] 201
rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 245
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071299 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071299
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071299/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071299
Building REAL250005071300
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071300'
/scratch/stefan/7916153/working/building/REAL250005071300 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071300

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071300/0 /scratch/stefan/7916153/working/building/REAL250005071300 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 426)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/426
`/scratch/stefan/7916153/working/3D/426' -> `0.mol2'
Preparing input files

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

`REAL250005071300.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071300.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071300/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071300 none COCC=CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 99, 99, 82, 55, 82, 55, 55, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 55, 138, 138, 138, 138, 138, 99, 99, 55, 55, 55, 19, 19, 19, 1, 55, 55] 138
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: 487
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071300 none COCC=CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [38, 21, 10, 10, 3, 1, 3, 1, 1, 1, 1, 11, 11, 38, 38, 55, 55, 55, 55, 55, 1, 38, 38, 38, 21, 21, 9, 10, 1, 1, 1, 11, 11, 11, 55, 1, 1] 138
rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 221
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071300 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071300
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071300/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071300
Building REAL250005071301
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071301'
/scratch/stefan/7916153/working/building/REAL250005071301 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071301

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071301/0 /scratch/stefan/7916153/working/building/REAL250005071301 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 427)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/427
`/scratch/stefan/7916153/working/3D/427' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)COC2)C1)

`REAL250005071301.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071301.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071301/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071301 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)COC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 20, 20, 36, 36, 36, 36, 36, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 1, 9, 9, 9, 36, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1] 73
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 118
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071301 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)COC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 36, 36, 36, 58, 58, 73, 73, 73, 73, 36, 22, 22, 22, 1, 36, 36, 36, 73, 73, 73, 73, 73, 73, 73, 36, 36] 73
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 233
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071301 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)COC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [35, 13, 35, 58, 58, 73, 73, 73, 73, 73, 13, 13, 4, 1, 4, 1, 1, 1, 1, 1, 13, 35, 35, 35, 73, 13, 13, 13, 2, 2, 2, 1, 1, 1, 1, 13, 13] 73
rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 188
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071301 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071301
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071301/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071301
Building REAL250005071302
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071302'
/scratch/stefan/7916153/working/building/REAL250005071302 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071302

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071302/0 /scratch/stefan/7916153/working/building/REAL250005071302 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 428)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/428
`/scratch/stefan/7916153/working/3D/428' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCO2)C1)

`REAL250005071302.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071302.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071302/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071302 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 12, 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, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 22, 22, 63, 63, 63, 63, 63, 1, 1, 1, 1, 4, 4, 23, 23, 23, 1, 9, 9, 9, 63, 1, 1, 1, 23, 23, 23, 23, 23, 1, 1] 142
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 19, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 173
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071302 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 12, 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, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 63, 63, 63, 87, 87, 142, 142, 142, 63, 34, 34, 34, 1, 63, 63, 63, 142, 142, 142, 142, 142, 63, 63] 142
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 465
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071302 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 12, 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, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [75, 23, 75, 128, 128, 142, 142, 142, 142, 142, 23, 23, 11, 1, 11, 1, 1, 1, 1, 23, 75, 75, 75, 142, 23, 23, 23, 1, 1, 1, 1, 1, 23, 23] 142
rigid atoms, others: [13, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33])
total number of confs: 375
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071302 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071302
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071302/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071302
Building REAL250005071303
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071303'
/scratch/stefan/7916153/working/building/REAL250005071303 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071303

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071303/0 /scratch/stefan/7916153/working/building/REAL250005071303 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 429)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/429
`/scratch/stefan/7916153/working/3D/429' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCN=[N+]=[N-])C1)

`REAL250005071303.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071303.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071303/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071303 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCN=[N+]=[N-])C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 14, 14, 28, 28, 28, 28, 28, 1, 1, 1, 1, 3, 3, 17, 35, 99, 99, 1, 6, 6, 6, 28, 1, 1, 1, 17, 17, 35, 35, 1, 1] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 295
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071303 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCN=[N+]=[N-])C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 28, 28, 28, 41, 41, 122, 137, 201, 201, 28, 18, 18, 18, 1, 28, 28, 28, 122, 122, 137, 137, 28, 28] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 652
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071303 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071303
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071303/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071303
Building REAL250005071304
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071304'
/scratch/stefan/7916153/working/building/REAL250005071304 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071304

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071304/0 /scratch/stefan/7916153/working/building/REAL250005071304 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 430)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/430
`/scratch/stefan/7916153/working/3D/430' -> `0.mol2'
Preparing input files

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

`REAL250005071304.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071304.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071304/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071304 none C#CCOCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 116, 37, 28, 37, 28, 28, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 28, 201, 201, 201, 116, 116, 28, 28, 28, 13, 13, 13, 1, 28, 28] 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: 689
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071304 none C#CCOCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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: [105, 105, 59, 21, 3, 1, 3, 1, 1, 1, 1, 9, 9, 18, 18, 28, 28, 28, 28, 28, 1, 105, 105, 105, 21, 21, 1, 1, 1, 9, 9, 9, 28, 1, 1] 201
rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 20, 26, 27, 28] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30, 31, 32])
total number of confs: 429
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071304 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071304
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071304/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071304
Building REAL250005071305
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071305'
/scratch/stefan/7916153/working/building/REAL250005071305 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071305

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071305/0 /scratch/stefan/7916153/working/building/REAL250005071305 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 431)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/431
`/scratch/stefan/7916153/working/3D/431' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)O)C1)

`REAL250005071305.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071305.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071305/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071305 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)O)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7]
1  hydrogens need rotated
387  conformations in input
total number of sets (complete confs): 387
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 32, 32, 63, 63, 63, 63, 63, 1, 1, 1, 1, 7, 7, 20, 20, 20, 1, 9, 9, 9, 63, 1, 1, 1, 20, 20, 20, 20, 20, 20, 60, 1, 1] 387
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 19, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 255
number of broken/clashed sets: 301
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071305 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)O)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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, 7, 7]
1  hydrogens need rotated
387  conformations in input
total number of sets (complete confs): 387
using faster count positions algorithm for large data
unique positions, atoms: [31, 10, 1, 10, 1, 1, 1, 1, 1, 1, 31, 63, 63, 63, 87, 87, 129, 129, 129, 63, 31, 31, 31, 1, 63, 63, 63, 129, 129, 129, 129, 129, 129, 387, 63, 63] 387
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 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: 876
number of broken/clashed sets: 301
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071305 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071305
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071305/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071305
Building REAL250005071306
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071306'
/scratch/stefan/7916153/working/building/REAL250005071306 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071306

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071306/0 /scratch/stefan/7916153/working/building/REAL250005071306 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 432)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/432
`/scratch/stefan/7916153/working/3D/432' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071306.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071306.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071306/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071306 none CC1=CC1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 6, 1, 6, 1, 1, 1, 1, 11, 11, 37, 37, 66, 66, 66, 66, 66, 1, 25, 25, 25, 25, 25, 1, 1, 1, 11, 11, 11, 66, 1, 1] 201
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 19, 25, 26, 27] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 193
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071306 none CC1=CC1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 11, 11, 25, 25, 25, 101, 101, 185, 185, 201, 201, 201, 201, 201, 25, 2, 2, 2, 1, 1, 25, 25, 25, 101, 101, 101, 201, 25, 25] 201
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: 539
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071306 none CC1=CC1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 95, 66, 95, 66, 66, 26, 9, 26, 1, 9, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 201, 66, 66, 66, 26, 26, 26, 1, 66, 66] 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])
total number of confs: 609
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071306 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071306
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071306/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071306
Building REAL250005071307
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071307'
/scratch/stefan/7916153/working/building/REAL250005071307 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071307

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071307/0 /scratch/stefan/7916153/working/building/REAL250005071307 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 433)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/433
`/scratch/stefan/7916153/working/3D/433' -> `0.mol2'
Preparing input files

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

`REAL250005071307.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071307.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071307/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071307 none CN(C)C(=O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 8, 5, 1, 11, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 55, 55, 38, 55, 31, 38, 31, 31, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 31, 55, 55, 55, 55, 55, 55, 31, 31, 31, 20, 20, 20, 1, 31, 31] 55
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: 181
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071307 none CN(C)C(=O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 8, 5, 1, 11, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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: [19, 18, 19, 5, 18, 1, 5, 1, 1, 1, 1, 9, 9, 16, 16, 31, 31, 31, 31, 31, 1, 19, 19, 19, 19, 19, 19, 1, 1, 1, 9, 9, 9, 31, 1, 1] 55
rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071307 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071307
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071307/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071307
Building REAL250005071308
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071308'
/scratch/stefan/7916153/working/building/REAL250005071308 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071308

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071308/0 /scratch/stefan/7916153/working/building/REAL250005071308 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 434)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/434
`/scratch/stefan/7916153/working/3D/434' -> `0.mol2'
Preparing input files

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

`REAL250005071308.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071308.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071308/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071308 none CSC=CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 131, 131, 95, 65, 95, 65, 65, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 65, 144, 144, 144, 131, 131, 65, 65, 65, 19, 19, 19, 1, 65, 65] 144
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: 445
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071308 none CSC=CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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: [37, 14, 14, 3, 1, 3, 1, 1, 1, 1, 11, 11, 39, 39, 65, 65, 65, 65, 65, 1, 37, 37, 37, 13, 14, 1, 1, 1, 11, 11, 11, 65, 1, 1] 144
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 19, 25, 26, 27] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 199
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071308 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071308
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071308/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071308
Building REAL250005071309
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071309'
/scratch/stefan/7916153/working/building/REAL250005071309 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071309

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071309/0 /scratch/stefan/7916153/working/building/REAL250005071309 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 435)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/435
`/scratch/stefan/7916153/working/3D/435' -> `0.mol2'
Preparing input files

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

`REAL250005071309.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071309.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071309/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071309 none CCC(C)(O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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
282  conformations in input
total number of sets (complete confs): 282
using faster count positions algorithm for large data
unique positions, atoms: [92, 90, 52, 90, 90, 38, 52, 38, 38, 18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 38, 94, 94, 94, 94, 94, 90, 90, 90, 270, 38, 38, 38, 18, 18, 18, 1, 38, 38] 282
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: 639
number of broken/clashed sets: 183
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071309 none CCC(C)(O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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
282  conformations in input
total number of sets (complete confs): 282
using faster count positions algorithm for large data
unique positions, atoms: [30, 21, 6, 21, 21, 1, 6, 1, 1, 1, 1, 7, 7, 20, 20, 38, 38, 38, 38, 38, 1, 32, 32, 32, 32, 32, 21, 21, 21, 63, 1, 1, 1, 7, 7, 7, 38, 1, 1] 282
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 287
number of broken/clashed sets: 183
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071309 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071309
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071309/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071309
Building REAL250005071310
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071310'
/scratch/stefan/7916153/working/building/REAL250005071310 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL250005071310

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071310/0 /scratch/stefan/7916153/working/building/REAL250005071310 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 436)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/436
`/scratch/stefan/7916153/working/3D/436' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@H+](C)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071310.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071310.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071310/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071310 none CC[N@H+](C)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 85, 75, 85, 85, 29, 26, 29, 26, 26, 15, 8, 15, 1, 8, 1, 1, 1, 1, 1, 1, 26, 86, 86, 86, 86, 86, 85, 85, 85, 75, 75, 26, 26, 26, 15, 15, 15, 1, 26, 26] 86
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: 326
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071310 none CC[N@H+](C)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [55, 47, 22, 47, 47, 6, 1, 6, 1, 1, 1, 1, 8, 8, 12, 12, 26, 26, 26, 26, 26, 1, 55, 55, 55, 55, 55, 47, 47, 47, 22, 22, 1, 1, 1, 8, 8, 8, 26, 1, 1] 86
rigid atoms, others: [32, 33, 34, 6, 39, 8, 9, 10, 11, 40, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 283
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071310 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071310/1 /scratch/stefan/7916153/working/building/REAL250005071310 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 437)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/437
`/scratch/stefan/7916153/working/3D/437' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@@H+](C)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071310.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071310.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071310/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071310 none CC[N@@H+](C)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 76, 83, 83, 24, 21, 24, 21, 21, 14, 8, 14, 1, 8, 1, 1, 1, 1, 1, 1, 21, 86, 86, 86, 86, 86, 83, 83, 83, 76, 76, 21, 21, 21, 14, 14, 14, 1, 21, 21] 86
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: 348
number of broken/clashed sets: 83
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071310 none CC[N@@H+](C)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [51, 44, 24, 44, 44, 6, 1, 6, 1, 1, 1, 1, 7, 7, 11, 11, 21, 21, 21, 21, 21, 1, 51, 51, 51, 51, 51, 44, 44, 44, 24, 24, 1, 1, 1, 7, 7, 7, 21, 1, 1] 86
rigid atoms, others: [32, 33, 34, 6, 39, 8, 9, 10, 11, 40, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38])
total number of confs: 267
number of broken/clashed sets: 83
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071310 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `2'
/scratch/stefan/7916153/working/building/REAL250005071310/2 /scratch/stefan/7916153/working/building/REAL250005071310 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 2 (index: 438)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/438
`/scratch/stefan/7916153/working/3D/438' -> `2.mol2'
Preparing input files

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

`REAL250005071310.mol2' -> `2.mol2'
`temp.mol2' -> `REAL250005071310.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071310/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071310 none CCN(C)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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', 'H']
dock atom type numbers: [5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 174, 197, 72, 46, 72, 46, 46, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 46, 201, 201, 201, 201, 201, 197, 197, 197, 174, 174, 46, 46, 46, 20, 20, 20, 1, 46, 46] 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: 770
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071310 none CCN(C)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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', 'H']
dock atom type numbers: [5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 49, 23, 49, 5, 1, 5, 1, 1, 1, 1, 9, 9, 30, 30, 46, 46, 46, 46, 46, 1, 60, 60, 60, 60, 60, 49, 49, 49, 23, 23, 1, 1, 1, 9, 9, 9, 46, 1, 1] 201
rigid atoms, others: [32, 33, 5, 38, 7, 8, 9, 10, 39, 20, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37])
total number of confs: 326
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071310 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071310
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
2: /scratch/stefan/7916153/working/building/REAL250005071310/2.*
1: /scratch/stefan/7916153/working/building/REAL250005071310/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071310/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071310
Building REAL250005071311
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071311'
/scratch/stefan/7916153/working/building/REAL250005071311 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071311

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071311/0 /scratch/stefan/7916153/working/building/REAL250005071311 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 439)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/439
`/scratch/stefan/7916153/working/3D/439' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)C1)

`REAL250005071311.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071311.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071311/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071311 none C=C1CC(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)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.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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 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, 7, 6, 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
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 6, 1, 6, 1, 1, 1, 1, 7, 7, 32, 32, 67, 67, 67, 67, 67, 1, 22, 22, 22, 22, 22, 22, 1, 1, 1, 7, 7, 7, 67, 1, 1, 22, 22] 148
rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 19, 26, 27, 28] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 35, 36])
total number of confs: 185
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071311 none C=C1CC(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)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.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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 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, 7, 6, 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
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 22, 22, 22, 70, 70, 133, 133, 148, 148, 148, 148, 148, 22, 1, 1, 1, 1, 1, 1, 22, 22, 22, 70, 70, 70, 148, 22, 22, 1, 1] 148
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: 384
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071311 none C=C1CC(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)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.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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 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, 7, 6, 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
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [148, 148, 148, 99, 67, 99, 67, 67, 25, 10, 25, 1, 10, 1, 1, 1, 1, 1, 1, 67, 148, 148, 148, 148, 148, 148, 67, 67, 67, 25, 25, 25, 1, 67, 67, 148, 148] 148
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: 471
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071311 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071311
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071311/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071311
Building REAL250005071312
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071312'
/scratch/stefan/7916153/working/building/REAL250005071312 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071312

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071312/0 /scratch/stefan/7916153/working/building/REAL250005071312 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 440)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/440
`/scratch/stefan/7916153/working/3D/440' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCC2F)C1)

`REAL250005071312.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071312.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071312/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071312 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCC2F)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 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, 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
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 22, 22, 56, 56, 56, 56, 56, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 1, 9, 9, 9, 56, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1] 142
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33])
total number of confs: 158
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071312 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCC2F)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 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, 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
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [32, 10, 1, 10, 1, 1, 1, 1, 1, 1, 32, 56, 56, 56, 78, 78, 142, 142, 142, 142, 56, 32, 32, 32, 1, 56, 56, 56, 142, 142, 142, 142, 142, 142, 56, 56] 142
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 441
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071312 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CCC2F)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 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, 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
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [71, 21, 71, 116, 116, 142, 142, 142, 142, 142, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 21, 71, 71, 71, 142, 21, 21, 21, 1, 1, 1, 1, 1, 1, 21, 21] 142
rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35])
total number of confs: 375
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071312 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071312
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071312/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071312
Building REAL250005071313
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071313'
/scratch/stefan/7916153/working/building/REAL250005071313 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071313

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071313/0 /scratch/stefan/7916153/working/building/REAL250005071313 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 441)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/441
`/scratch/stefan/7916153/working/3D/441' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CNC=N2)C1)

`REAL250005071313.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071313.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071313/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071313 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CNC=N2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 20, 20, 40, 40, 40, 40, 40, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 1, 8, 8, 8, 40, 1, 1, 1, 17, 17, 17, 1, 1] 82
rigid atoms, others: [32, 1, 10, 11, 12, 13, 20, 25, 26, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 109
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071313 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CNC=N2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 40, 40, 40, 58, 58, 82, 82, 82, 82, 40, 25, 25, 25, 1, 40, 40, 40, 82, 82, 82, 40, 40] 82
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 226
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071313 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CNC=N2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 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, 3, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [43, 17, 43, 74, 74, 82, 82, 82, 82, 82, 17, 17, 10, 1, 10, 1, 1, 1, 1, 1, 17, 43, 43, 43, 82, 17, 17, 17, 1, 1, 1, 17, 17] 82
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32])
total number of confs: 215
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071313 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071313/1 /scratch/stefan/7916153/working/building/REAL250005071313 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 442)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/442
`/scratch/stefan/7916153/working/3D/442' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CN=CN2)C1)

`REAL250005071313.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071313.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071313/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071313 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CN=CN2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [6, 1, 6, 17, 17, 34, 34, 34, 34, 34, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 1, 7, 7, 7, 34, 1, 1, 1, 24, 24, 24, 1, 1] 89
rigid atoms, others: [32, 1, 10, 11, 12, 13, 20, 25, 26, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 110
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071313 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CN=CN2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 34, 34, 34, 48, 48, 89, 89, 89, 89, 34, 21, 21, 21, 1, 34, 34, 34, 89, 89, 89, 34, 34] 89
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 230
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071313 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CN=CN2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [53, 24, 53, 73, 73, 89, 89, 89, 89, 89, 24, 24, 11, 1, 11, 1, 1, 1, 1, 1, 24, 53, 53, 53, 89, 24, 24, 24, 1, 1, 1, 24, 24] 89
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32])
total number of confs: 226
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071313 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071313
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071313/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071313/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071313
Building REAL250005071314
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071314'
/scratch/stefan/7916153/working/building/REAL250005071314 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071314

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071314/0 /scratch/stefan/7916153/working/building/REAL250005071314 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 443)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/443
`/scratch/stefan/7916153/working/3D/443' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(Cl)CC2)C1)

`REAL250005071314.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071314.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071314/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071314 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(Cl)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 16, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 24, 24, 53, 53, 53, 53, 53, 1, 1, 1, 1, 6, 6, 21, 21, 21, 1, 9, 9, 9, 53, 1, 1, 1, 21, 21, 21, 21, 1, 1] 130
rigid atoms, others: [32, 1, 10, 11, 12, 13, 19, 24, 25, 26, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 160
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071314 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(Cl)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 16, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 53, 53, 53, 80, 80, 130, 130, 130, 53, 29, 29, 29, 1, 53, 53, 53, 130, 130, 130, 130, 53, 53] 130
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 421
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071314 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(Cl)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 16, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [68, 21, 68, 110, 110, 130, 130, 130, 130, 130, 21, 21, 8, 1, 8, 1, 1, 1, 1, 21, 68, 68, 68, 130, 21, 21, 21, 1, 1, 1, 1, 21, 21] 130
rigid atoms, others: [13, 15, 16, 17, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32])
total number of confs: 323
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071314 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071314
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071314/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071314
Building REAL250005071315
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071315'
/scratch/stefan/7916153/working/building/REAL250005071315 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071315

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071315/0 /scratch/stefan/7916153/working/building/REAL250005071315 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 444)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/444
`/scratch/stefan/7916153/working/3D/444' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CCCO2)C1)

`REAL250005071315.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071315.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071315/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071315 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CCCO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 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, 3, 7, 3, 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]
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: [9, 1, 9, 23, 23, 49, 49, 49, 49, 49, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 1, 9, 9, 9, 49, 1, 1, 1, 26, 26, 26, 26, 26, 1, 1] 109
rigid atoms, others: [1, 34, 33, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32])
total number of confs: 132
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071315 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CCCO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 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, 3, 7, 3, 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]
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, 10, 1, 10, 1, 1, 1, 1, 1, 1, 31, 49, 49, 49, 69, 69, 109, 109, 109, 109, 49, 31, 31, 31, 1, 49, 49, 49, 109, 109, 109, 109, 109, 49, 49] 109
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 275
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071315 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CCCO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 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, 3, 7, 3, 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]
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: [64, 26, 64, 98, 98, 109, 109, 109, 109, 109, 26, 26, 12, 1, 12, 1, 1, 1, 1, 1, 26, 64, 64, 64, 109, 26, 26, 26, 1, 1, 1, 1, 1, 26, 26] 109
rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34])
total number of confs: 279
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071315 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071315
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071315/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071315
Building REAL250005071316
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071316'
/scratch/stefan/7916153/working/building/REAL250005071316 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071316

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071316/0 /scratch/stefan/7916153/working/building/REAL250005071316 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 445)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/445
`/scratch/stefan/7916153/working/3D/445' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC[C@H](O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071316.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071316.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071316/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071316 none CCC[C@H](O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens 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, 195, 141, 62, 141, 141, 44, 62, 44, 44, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 44, 201, 201, 201, 201, 201, 195, 195, 423, 44, 44, 44, 21, 21, 21, 1, 44, 44] 603
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: 1299
number of broken/clashed sets: 52
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071316 none CCC[C@H](O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [59, 49, 20, 5, 20, 20, 1, 5, 1, 1, 1, 1, 9, 9, 25, 25, 44, 44, 44, 44, 44, 1, 59, 59, 59, 57, 59, 52, 52, 60, 1, 1, 1, 9, 9, 9, 44, 1, 1] 603
rigid atoms, others: [32, 37, 6, 8, 9, 10, 11, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 415
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071316 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071316
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071316/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071316
Building REAL250005071317
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071317'
/scratch/stefan/7916153/working/building/REAL250005071317 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071317

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071317/0 /scratch/stefan/7916153/working/building/REAL250005071317 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 446)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/446
`/scratch/stefan/7916153/working/3D/446' -> `0.mol2'
Preparing input files

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

`REAL250005071317.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071317.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071317/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071317 none CC(C)[C@H](O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [199, 187, 201, 94, 187, 187, 65, 94, 65, 65, 25, 10, 25, 1, 10, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 201, 201, 561, 65, 65, 65, 25, 25, 25, 1, 65, 65] 603
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: 1367
number of broken/clashed sets: 63
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071317 none CC(C)[C@H](O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [57, 31, 60, 6, 31, 31, 1, 6, 1, 1, 1, 1, 9, 9, 31, 31, 65, 65, 65, 65, 65, 1, 61, 61, 61, 61, 61, 61, 61, 93, 1, 1, 1, 9, 9, 9, 65, 1, 1] 603
rigid atoms, others: [32, 37, 6, 8, 9, 10, 11, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 484
number of broken/clashed sets: 63
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071317 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071317
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071317/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071317
Building REAL250005071318
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071318'
/scratch/stefan/7916153/working/building/REAL250005071318 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071318

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071318/0 /scratch/stefan/7916153/working/building/REAL250005071318 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 447)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/447
`/scratch/stefan/7916153/working/3D/447' -> `0.mol2'
Preparing input files

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

`REAL250005071318.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071318.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071318/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071318 none CCOC=CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [184, 184, 139, 139, 95, 63, 95, 63, 63, 18, 8, 18, 1, 8, 1, 1, 1, 1, 1, 1, 63, 184, 184, 184, 184, 184, 139, 139, 63, 63, 63, 18, 18, 18, 1, 63, 63] 184
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: 516
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071318 none CCOC=CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [47, 36, 16, 16, 3, 1, 3, 1, 1, 1, 1, 11, 11, 40, 40, 63, 63, 63, 63, 63, 1, 47, 47, 47, 47, 47, 15, 16, 1, 1, 1, 11, 11, 11, 63, 1, 1] 184
rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 266
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071318 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071318
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071318/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071318
Building REAL250005071319
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071319'
/scratch/stefan/7916153/working/building/REAL250005071319 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071319

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071319/0 /scratch/stefan/7916153/working/building/REAL250005071319 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 448)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/448
`/scratch/stefan/7916153/working/3D/448' -> `0.mol2'
Preparing input files

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

`REAL250005071319.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071319.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071319/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071319 none C[C@@H](O)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
381  conformations in input
total number of sets (complete confs): 381
using faster count positions algorithm for large data
unique positions, atoms: [127, 67, 127, 127, 53, 67, 53, 53, 23, 10, 23, 1, 10, 1, 1, 1, 1, 1, 1, 53, 127, 127, 127, 381, 53, 53, 53, 23, 23, 23, 1, 53, 53] 381
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: 879
number of broken/clashed sets: 55
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071319 none C[C@@H](O)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
381  conformations in input
total number of sets (complete confs): 381
using faster count positions algorithm for large data
unique positions, atoms: [21, 5, 21, 21, 1, 5, 1, 1, 1, 1, 10, 10, 34, 34, 53, 53, 53, 53, 53, 1, 21, 21, 21, 63, 1, 1, 1, 11, 11, 11, 53, 1, 1] 381
rigid atoms, others: [32, 4, 6, 7, 8, 9, 19, 24, 25, 26, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 253
number of broken/clashed sets: 55
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071319 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071319
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071319/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071319
Building REAL250005071320
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071320'
/scratch/stefan/7916153/working/building/REAL250005071320 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071320

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071320/0 /scratch/stefan/7916153/working/building/REAL250005071320 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 449)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/449
`/scratch/stefan/7916153/working/3D/449' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCCCF)C1)

`REAL250005071320.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071320.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071320/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071320 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCCCF)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 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, 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, 7, 7]
0  hydrogens 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, 18, 18, 34, 34, 34, 34, 34, 1, 1, 1, 1, 3, 3, 17, 25, 36, 70, 1, 9, 9, 9, 34, 1, 1, 1, 17, 17, 31, 31, 36, 36, 70, 70, 1, 1] 201
rigid atoms, others: [1, 36, 37, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 438
number of broken/clashed sets: 131
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071320 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCCCF)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 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, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 34, 34, 34, 45, 45, 154, 181, 201, 201, 34, 19, 19, 19, 1, 34, 34, 34, 154, 154, 196, 196, 201, 201, 201, 201, 34, 34] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 922
number of broken/clashed sets: 131
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071320 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071320
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071320/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071320
Building REAL250005071321
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071321'
/scratch/stefan/7916153/working/building/REAL250005071321 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071321

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071321/0 /scratch/stefan/7916153/working/building/REAL250005071321 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 450)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/450
`/scratch/stefan/7916153/working/3D/450' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CCO)C1)

`REAL250005071321.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071321.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071321/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071321 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CCO)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 22, 22, 63, 63, 63, 63, 63, 1, 1, 1, 1, 7, 7, 24, 24, 72, 1, 8, 8, 8, 63, 1, 1, 1, 24, 23, 72, 72, 216, 1, 1] 603
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 19, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 567
number of broken/clashed sets: 78
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071321 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CCO)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 63, 63, 63, 103, 103, 189, 189, 201, 63, 29, 29, 29, 1, 63, 63, 63, 189, 189, 201, 201, 603, 63, 63] 603
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 1268
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071321 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071321
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071321/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071321
Building REAL250005071322
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071322'
/scratch/stefan/7916153/working/building/REAL250005071322 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071322

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071322/0 /scratch/stefan/7916153/working/building/REAL250005071322 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 451)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/451
`/scratch/stefan/7916153/working/3D/451' -> `0.mol2'
Preparing input files

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

`REAL250005071322.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071322.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071322/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071322 none COC(C)(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [123, 120, 89, 120, 120, 62, 89, 62, 62, 24, 10, 24, 1, 10, 1, 1, 1, 1, 1, 1, 62, 123, 123, 123, 120, 120, 120, 120, 120, 120, 62, 62, 62, 24, 24, 24, 1, 62, 62] 123
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: 432
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071322 none COC(C)(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [39, 18, 7, 18, 18, 1, 7, 1, 1, 1, 1, 11, 11, 36, 36, 62, 62, 62, 62, 62, 1, 39, 39, 39, 18, 18, 18, 18, 18, 18, 1, 1, 1, 11, 11, 11, 62, 1, 1] 123
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 220
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071322 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071322
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071322/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071322
Building REAL250005071323
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071323'
/scratch/stefan/7916153/working/building/REAL250005071323 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071323

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071323/0 /scratch/stefan/7916153/working/building/REAL250005071323 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 452)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/452
`/scratch/stefan/7916153/working/3D/452' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCCCO)C1)

`REAL250005071323.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071323.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071323/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071323 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCCCO)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [3, 1, 3, 7, 7, 14, 14, 14, 14, 14, 1, 1, 1, 1, 2, 2, 16, 20, 25, 38, 1, 3, 3, 3, 14, 1, 1, 1, 16, 16, 24, 24, 25, 25, 38, 38, 114, 1, 1] 177
rigid atoms, others: [1, 37, 38, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 345
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071323 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCCCO)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 20, 20, 49, 54, 59, 59, 14, 13, 13, 13, 1, 14, 14, 14, 49, 49, 58, 58, 59, 59, 59, 59, 177, 14, 14] 177
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 434
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071323 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071323
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071323/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071323
Building REAL250005071324
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071324'
/scratch/stefan/7916153/working/building/REAL250005071324 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071324

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071324/0 /scratch/stefan/7916153/working/building/REAL250005071324 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 453)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/453
`/scratch/stefan/7916153/working/3D/453' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(CO)CC2)C1)

`REAL250005071324.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071324.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071324/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071324 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(CO)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 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, 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, 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: [8, 1, 8, 25, 25, 65, 65, 65, 65, 65, 1, 1, 1, 1, 6, 6, 12, 40, 12, 12, 1, 9, 9, 9, 65, 1, 1, 1, 40, 40, 120, 12, 12, 12, 12, 1, 1] 543
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 376
number of broken/clashed sets: 93
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071324 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(CO)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 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, 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, 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: [27, 8, 1, 8, 1, 1, 1, 1, 1, 1, 27, 65, 65, 65, 104, 104, 173, 181, 173, 173, 65, 27, 27, 27, 1, 65, 65, 65, 181, 181, 543, 173, 173, 173, 173, 65, 65] 543
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 1170
number of broken/clashed sets: 93
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071324 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(CO)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 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, 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, 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: [47, 12, 47, 100, 100, 173, 173, 173, 173, 173, 12, 12, 5, 1, 5, 1, 1, 10, 1, 1, 12, 47, 47, 47, 173, 12, 12, 12, 10, 10, 30, 1, 1, 1, 1, 12, 12] 543
rigid atoms, others: [32, 33, 34, 13, 15, 16, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 432
number of broken/clashed sets: 93
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071324 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071324
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071324/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071324
Building REAL250005071325
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071325'
/scratch/stefan/7916153/working/building/REAL250005071325 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071325

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071325/0 /scratch/stefan/7916153/working/building/REAL250005071325 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 454)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/454
`/scratch/stefan/7916153/working/3D/454' -> `0.mol2'
Preparing input files

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

`REAL250005071325.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071325.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071325/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071325 none COC(F)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 12, 5, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [161, 160, 69, 160, 50, 69, 50, 50, 25, 10, 25, 1, 10, 1, 1, 1, 1, 1, 1, 50, 161, 161, 161, 160, 50, 50, 50, 25, 25, 25, 1, 50, 50] 161
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: 584
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071325 none COC(F)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 12, 5, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [87, 43, 6, 43, 1, 6, 1, 1, 1, 1, 8, 8, 22, 22, 50, 50, 50, 50, 50, 1, 87, 87, 87, 43, 1, 1, 1, 8, 8, 8, 50, 1, 1] 161
rigid atoms, others: [32, 4, 6, 7, 8, 9, 19, 24, 25, 26, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 303
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071325 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071325
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071325/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071325
Building REAL250005071326
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071326'
/scratch/stefan/7916153/working/building/REAL250005071326 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071326

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071326/0 /scratch/stefan/7916153/working/building/REAL250005071326 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 455)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/455
`/scratch/stefan/7916153/working/3D/455' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C23CC2CC3)C1)

`REAL250005071326.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071326.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071326/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071326 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C23CC2CC3)C1 NO_LONG_NAME
dock atom types: ['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.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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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: [7, 7, 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, 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: [8, 1, 8, 20, 20, 40, 40, 40, 40, 40, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 1, 8, 8, 8, 40, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 1, 1] 160
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 118
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071326 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C23CC2CC3)C1 NO_LONG_NAME
dock atom types: ['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.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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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: [7, 7, 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, 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: [25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 40, 40, 40, 60, 60, 160, 160, 160, 160, 40, 25, 25, 25, 1, 40, 40, 40, 160, 160, 160, 160, 160, 160, 160, 40, 40] 160
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 329
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071326 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C23CC2CC3)C1 NO_LONG_NAME
dock atom types: ['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.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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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: [7, 7, 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, 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: [66, 22, 66, 121, 121, 160, 160, 160, 160, 160, 22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 22, 66, 66, 66, 160, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 22, 22] 160
rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36])
total number of confs: 392
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071326 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071326
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071326/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071326
Building REAL250005071327
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071327'
/scratch/stefan/7916153/working/building/REAL250005071327 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071327

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071327/0 /scratch/stefan/7916153/working/building/REAL250005071327 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 456)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/456
`/scratch/stefan/7916153/working/3D/456' -> `0.mol2'
Preparing input files

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

`REAL250005071327.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071327.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071327/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071327 none C=C[C@H](C)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 183, 201, 201, 57, 46, 57, 46, 46, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 46, 201, 201, 201, 201, 201, 201, 183, 183, 46, 46, 46, 21, 21, 21, 1, 46, 46] 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: 774
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071327 none C=C[C@H](C)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 45, 16, 45, 44, 2, 1, 2, 1, 1, 1, 1, 9, 9, 28, 28, 46, 46, 46, 46, 46, 1, 66, 66, 66, 45, 45, 45, 16, 16, 1, 1, 1, 9, 9, 9, 46, 1, 1] 201
rigid atoms, others: [32, 37, 6, 8, 9, 10, 11, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 364
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071327 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071327
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071327/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071327
Building REAL250005071328
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071328'
/scratch/stefan/7916153/working/building/REAL250005071328 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071328

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071328/0 /scratch/stefan/7916153/working/building/REAL250005071328 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 457)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/457
`/scratch/stefan/7916153/working/3D/457' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CC2CC2)C1)

`REAL250005071328.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071328.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071328/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071328 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CC2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 26, 26, 62, 62, 62, 62, 62, 1, 1, 1, 1, 7, 7, 22, 22, 67, 67, 1, 8, 8, 8, 62, 1, 1, 1, 22, 21, 67, 67, 67, 67, 67, 1, 1] 201
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 285
number of broken/clashed sets: 57
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071328 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CC2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 8, 1, 8, 1, 1, 1, 1, 1, 1, 28, 62, 62, 62, 87, 87, 151, 151, 201, 201, 62, 28, 28, 28, 1, 62, 62, 62, 151, 151, 201, 201, 201, 201, 201, 62, 62] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 665
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071328 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C=CC2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [133, 67, 133, 195, 195, 201, 201, 201, 201, 201, 67, 67, 38, 9, 38, 9, 1, 1, 1, 1, 67, 133, 133, 133, 201, 66, 67, 67, 9, 9, 1, 1, 1, 1, 1, 67, 67] 201
rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36])
total number of confs: 568
number of broken/clashed sets: 57
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071328 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071328
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071328/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071328
Building REAL250005071329
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071329'
/scratch/stefan/7916153/working/building/REAL250005071329 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071329

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071329/0 /scratch/stefan/7916153/working/building/REAL250005071329 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 458)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/458
`/scratch/stefan/7916153/working/3D/458' -> `0.mol2'
Preparing input files

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

`REAL250005071329.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071329.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071329/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071329 none CC=C(CC)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [138, 138, 87, 138, 201, 64, 87, 64, 64, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 64, 138, 138, 138, 138, 201, 201, 201, 201, 201, 64, 64, 64, 21, 21, 21, 1, 64, 64] 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: 833
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071329 none CC=C(CC)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 5, 17, 32, 1, 5, 1, 1, 1, 1, 10, 10, 37, 37, 64, 64, 64, 64, 64, 1, 17, 17, 17, 17, 32, 32, 32, 32, 32, 1, 1, 1, 10, 10, 10, 64, 1, 1] 201
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 251
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071329 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071329
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071329/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071329
Building REAL250005071330
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071330'
/scratch/stefan/7916153/working/building/REAL250005071330 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071330

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071330/0 /scratch/stefan/7916153/working/building/REAL250005071330 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 459)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/459
`/scratch/stefan/7916153/working/3D/459' -> `0.mol2'
Preparing input files

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

`REAL250005071330.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071330.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071330/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071330 none C=CC(C)(O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 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
375  conformations in input
total number of sets (complete confs): 375
using faster count positions algorithm for large data
unique positions, atoms: [125, 125, 70, 125, 125, 51, 70, 51, 51, 24, 9, 24, 1, 9, 1, 1, 1, 1, 1, 1, 51, 125, 125, 125, 125, 125, 125, 375, 51, 51, 51, 24, 24, 24, 1, 51, 51] 375
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: 843
number of broken/clashed sets: 106
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071330 none C=CC(C)(O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 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
375  conformations in input
total number of sets (complete confs): 375
using faster count positions algorithm for large data
unique positions, atoms: [47, 29, 6, 29, 29, 1, 6, 1, 1, 1, 1, 8, 8, 26, 26, 51, 51, 51, 51, 51, 1, 47, 47, 47, 29, 29, 29, 87, 1, 1, 1, 8, 8, 8, 51, 1, 1] 375
rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 346
number of broken/clashed sets: 106
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071330 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071330
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071330/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071330
Building REAL250005071331
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071331'
/scratch/stefan/7916153/working/building/REAL250005071331 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071331

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071331/0 /scratch/stefan/7916153/working/building/REAL250005071331 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 460)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/460
`/scratch/stefan/7916153/working/3D/460' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CCC2)C1)

`REAL250005071331.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071331.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071331/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071331 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 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, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 23, 23, 44, 44, 44, 44, 44, 1, 1, 1, 1, 6, 6, 17, 17, 17, 1, 9, 9, 9, 44, 1, 1, 1, 17, 17, 17, 17, 17, 1, 1] 64
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 19, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 113
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071331 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 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, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 44, 44, 44, 64, 64, 64, 64, 64, 44, 24, 24, 24, 1, 44, 44, 44, 64, 64, 64, 64, 64, 44, 44] 64
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 207
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071331 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 5, 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, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [37, 16, 37, 55, 55, 64, 64, 64, 64, 64, 17, 17, 8, 1, 8, 1, 1, 1, 1, 17, 37, 37, 37, 64, 17, 17, 17, 1, 1, 1, 1, 1, 17, 17] 64
rigid atoms, others: [13, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33])
total number of confs: 163
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071331 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071331
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071331/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071331
Building REAL250005071332
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071332'
/scratch/stefan/7916153/working/building/REAL250005071332 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071332

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071332/0 /scratch/stefan/7916153/working/building/REAL250005071332 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 461)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/461
`/scratch/stefan/7916153/working/3D/461' -> `0.mol2'
Preparing input files

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

`REAL250005071332.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071332.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071332/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071332 none CON=CC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [168, 168, 168, 104, 69, 104, 69, 69, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 69, 168, 168, 168, 168, 69, 69, 69, 19, 19, 19, 1, 69, 69] 168
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: 545
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071332 none CON=CC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [38, 20, 20, 4, 1, 4, 1, 1, 1, 1, 11, 11, 42, 42, 69, 69, 69, 69, 69, 1, 38, 38, 38, 20, 1, 1, 1, 11, 11, 11, 69, 1, 1] 168
rigid atoms, others: [32, 4, 6, 7, 8, 9, 19, 24, 25, 26, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 221
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071332 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071332
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071332/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071332
Building REAL250005071333
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071333'
/scratch/stefan/7916153/working/building/REAL250005071333 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071333

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071333/0 /scratch/stefan/7916153/working/building/REAL250005071333 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 462)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/462
`/scratch/stefan/7916153/working/3D/462' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(F)CC2)C1)

`REAL250005071333.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071333.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071333/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071333 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(F)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 26, 26, 71, 71, 71, 71, 71, 1, 1, 1, 1, 6, 6, 25, 25, 25, 1, 9, 9, 9, 71, 1, 1, 1, 25, 25, 25, 25, 1, 1] 156
rigid atoms, others: [32, 1, 10, 11, 12, 13, 19, 24, 25, 26, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 192
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071333 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(F)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [33, 9, 1, 9, 1, 1, 1, 1, 1, 1, 33, 71, 71, 71, 107, 107, 156, 156, 156, 71, 33, 33, 33, 1, 71, 71, 71, 156, 156, 156, 156, 71, 71] 156
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 513
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071333 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(F)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [85, 25, 85, 140, 140, 156, 156, 156, 156, 156, 25, 25, 9, 1, 9, 1, 1, 1, 1, 25, 85, 85, 85, 156, 25, 25, 25, 1, 1, 1, 1, 25, 25] 156
rigid atoms, others: [13, 15, 16, 17, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32])
total number of confs: 406
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071333 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071333
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071333/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071333
Building REAL250005071334
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071334'
/scratch/stefan/7916153/working/building/REAL250005071334 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071334

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071334/0 /scratch/stefan/7916153/working/building/REAL250005071334 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 463)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/463
`/scratch/stefan/7916153/working/3D/463' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)COCCO)C1)

`REAL250005071334.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071334.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071334/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071334 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)COCCO)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens 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, 14, 14, 31, 31, 31, 31, 31, 1, 1, 1, 1, 3, 3, 11, 36, 58, 79, 1, 6, 6, 6, 31, 1, 1, 1, 11, 11, 58, 58, 79, 79, 237, 1, 1] 603
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 595
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071334 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)COCCO)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 31, 31, 31, 51, 51, 123, 174, 201, 201, 31, 19, 19, 19, 1, 31, 31, 31, 123, 123, 201, 201, 201, 201, 603, 31, 31] 603
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 1354
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071334 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071334
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071334/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071334
Building REAL250005071335
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071335'
/scratch/stefan/7916153/working/building/REAL250005071335 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071335

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071335/0 /scratch/stefan/7916153/working/building/REAL250005071335 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 464)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/464
`/scratch/stefan/7916153/working/3D/464' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)CF)C1)

`REAL250005071335.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071335.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071335/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071335 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)CF)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 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, 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, 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: [9, 1, 9, 22, 22, 59, 59, 59, 59, 59, 1, 1, 1, 1, 7, 7, 18, 18, 18, 44, 1, 9, 9, 9, 59, 1, 1, 1, 18, 18, 18, 18, 18, 18, 44, 44, 1, 1] 180
rigid atoms, others: [1, 36, 37, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 282
number of broken/clashed sets: 176
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071335 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C(C)(C)CF)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 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, 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, 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: [29, 8, 1, 8, 1, 1, 1, 1, 1, 1, 29, 59, 59, 59, 100, 100, 179, 179, 179, 180, 59, 29, 29, 29, 1, 59, 59, 59, 179, 179, 179, 179, 179, 179, 180, 180, 59, 59] 180
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 707
number of broken/clashed sets: 176
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071335 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071335
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071335/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071335
Building REAL250005071336
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071336'
/scratch/stefan/7916153/working/building/REAL250005071336 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071336

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071336/0 /scratch/stefan/7916153/working/building/REAL250005071336 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 465)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/465
`/scratch/stefan/7916153/working/3D/465' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NOCC2)C1)

`REAL250005071336.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071336.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071336/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071336 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NOCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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, 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: [9, 1, 9, 22, 22, 51, 51, 51, 51, 51, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 1, 9, 9, 9, 51, 1, 1, 1, 36, 36, 36, 36, 1, 1] 143
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 145
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071336 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NOCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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, 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: [29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 51, 51, 51, 77, 77, 143, 143, 143, 143, 51, 29, 29, 29, 1, 51, 51, 51, 143, 143, 143, 143, 51, 51] 143
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 343
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071336 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NOCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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, 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: [96, 36, 96, 137, 137, 143, 143, 143, 143, 143, 36, 36, 13, 1, 13, 1, 1, 1, 1, 1, 36, 96, 96, 96, 143, 36, 36, 36, 1, 1, 1, 1, 36, 36] 143
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 378
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071336 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071336
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071336/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071336
Building REAL250005071337
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071337'
/scratch/stefan/7916153/working/building/REAL250005071337 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071337

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071337/0 /scratch/stefan/7916153/working/building/REAL250005071337 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 466)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/466
`/scratch/stefan/7916153/working/3D/466' -> `0.mol2'
Preparing input files

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

`REAL250005071337.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071337.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071337/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071337 none COCC(O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 12, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 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, 199, 157, 68, 157, 49, 68, 49, 49, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 49, 201, 201, 201, 199, 199, 157, 471, 49, 49, 49, 21, 21, 21, 1, 49, 49] 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: 1322
number of broken/clashed sets: 69
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071337 none COCC(O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 12, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 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: [67, 35, 14, 3, 14, 1, 3, 1, 1, 1, 1, 9, 9, 29, 29, 49, 49, 49, 49, 49, 1, 67, 67, 67, 35, 35, 14, 42, 1, 1, 1, 9, 9, 9, 49, 1, 1] 603
rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 340
number of broken/clashed sets: 69
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071337 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071337
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071337/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071337
Building REAL250005071338
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071338'
/scratch/stefan/7916153/working/building/REAL250005071338 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071338

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071338/0 /scratch/stefan/7916153/working/building/REAL250005071338 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 467)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/467
`/scratch/stefan/7916153/working/3D/467' -> `0.mol2'
Preparing input files

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

`REAL250005071338.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071338.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071338/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071338 none C#CC(C)(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 75, 93, 93, 52, 75, 52, 52, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 52, 93, 93, 93, 93, 93, 93, 93, 52, 52, 52, 19, 19, 19, 1, 52, 52] 93
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: 325
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071338 none C#CC(C)(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 7, 13, 13, 1, 7, 1, 1, 1, 1, 11, 11, 35, 35, 52, 52, 52, 52, 52, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 11, 11, 11, 52, 1, 1] 93
rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 157
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071338 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071338
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071338/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071338
Building REAL250005071339
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071339'
/scratch/stefan/7916153/working/building/REAL250005071339 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071339

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071339/0 /scratch/stefan/7916153/working/building/REAL250005071339 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 468)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/468
`/scratch/stefan/7916153/working/3D/468' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)COC2CC2)C1)

`REAL250005071339.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071339.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071339/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071339 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)COC2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 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, 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, 7, 7, 7]
0  hydrogens 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, 15, 15, 29, 29, 29, 29, 29, 1, 1, 1, 1, 3, 3, 21, 61, 101, 101, 1, 7, 7, 7, 29, 1, 1, 1, 21, 21, 101, 101, 101, 101, 101, 1, 1] 201
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 327
number of broken/clashed sets: 49
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071339 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)COC2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 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, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 29, 29, 29, 40, 40, 133, 172, 201, 201, 29, 18, 18, 18, 1, 29, 29, 29, 133, 133, 201, 201, 201, 201, 201, 29, 29] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 663
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071339 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)COC2CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 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, 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, 7, 7, 7]
0  hydrogens 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, 101, 152, 201, 201, 201, 201, 201, 201, 201, 101, 101, 74, 22, 74, 5, 1, 1, 1, 1, 101, 152, 152, 152, 201, 101, 101, 101, 22, 22, 1, 1, 1, 1, 1, 101, 101] 201
rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36])
total number of confs: 609
number of broken/clashed sets: 49
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071339 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071339
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071339/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071339
Building REAL250005071340
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071340'
/scratch/stefan/7916153/working/building/REAL250005071340 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071340

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071340/0 /scratch/stefan/7916153/working/building/REAL250005071340 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 469)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/469
`/scratch/stefan/7916153/working/3D/469' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NC=CN2)C1)

`REAL250005071340.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071340.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071340/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071340 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NC=CN2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [8, 1, 8, 21, 21, 38, 38, 38, 38, 38, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 1, 9, 9, 9, 38, 1, 1, 1, 19, 19, 19, 1, 1] 59
rigid atoms, others: [32, 1, 10, 11, 12, 13, 20, 25, 26, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 114
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071340 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NC=CN2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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: [22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 38, 38, 38, 51, 51, 59, 59, 59, 59, 38, 22, 22, 22, 1, 38, 38, 38, 59, 59, 59, 38, 38] 59
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 179
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071340 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=NC=CN2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [32, 17, 32, 47, 47, 56, 56, 56, 56, 56, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 17, 32, 32, 32, 56, 17, 17, 17, 1, 1, 1, 17, 17] 56
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32])
total number of confs: 132
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071340 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071340
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071340/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071340
Building REAL250005071341
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071341'
/scratch/stefan/7916153/working/building/REAL250005071341 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071341

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071341/0 /scratch/stefan/7916153/working/building/REAL250005071341 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 470)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/470
`/scratch/stefan/7916153/working/3D/470' -> `0.mol2'
Preparing input files

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

`REAL250005071341.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071341.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071341/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071341 none CCCC=CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 128, 128, 82, 57, 82, 57, 57, 20, 9, 20, 1, 9, 1, 1, 1, 1, 1, 1, 57, 201, 201, 201, 201, 201, 186, 186, 128, 128, 57, 57, 57, 20, 20, 20, 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: 835
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071341 none CCCC=CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 11, 11, 3, 1, 3, 1, 1, 1, 1, 11, 11, 38, 38, 57, 57, 57, 57, 57, 1, 51, 51, 51, 51, 51, 37, 37, 10, 11, 1, 1, 1, 11, 11, 11, 57, 1, 1] 201
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 333
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071341 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071341
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071341/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071341
Building REAL250005071342
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071342'
/scratch/stefan/7916153/working/building/REAL250005071342 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071342

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071342/0 /scratch/stefan/7916153/working/building/REAL250005071342 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 471)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/471
`/scratch/stefan/7916153/working/3D/471' -> `0.mol2'
Preparing input files

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

`REAL250005071342.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071342.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071342/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071342 none CC=C(F)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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: [124, 124, 83, 124, 63, 83, 63, 63, 27, 10, 27, 1, 10, 1, 1, 1, 1, 1, 1, 63, 124, 124, 124, 124, 63, 63, 63, 27, 27, 27, 1, 63, 63] 124
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: 379
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071342 none CC=C(F)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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: [26, 26, 7, 26, 1, 7, 1, 1, 1, 1, 11, 11, 36, 36, 63, 63, 63, 63, 63, 1, 26, 26, 26, 25, 1, 1, 1, 11, 11, 11, 63, 1, 1] 124
rigid atoms, others: [32, 4, 6, 7, 8, 9, 19, 24, 25, 26, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 190
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071342 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071342
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071342/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071342
Building REAL250005071343
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071343'
/scratch/stefan/7916153/working/building/REAL250005071343 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071343

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071343/0 /scratch/stefan/7916153/working/building/REAL250005071343 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 472)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/472
`/scratch/stefan/7916153/working/3D/472' -> `0.mol2'
Preparing input files

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

`REAL250005071343.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071343.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071343/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071343 none CCC(CO)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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
567  conformations in input
total number of sets (complete confs): 567
using faster count positions algorithm for large data
unique positions, atoms: [169, 157, 86, 157, 183, 57, 86, 57, 57, 22, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 57, 182, 182, 182, 182, 182, 157, 183, 183, 549, 57, 57, 57, 22, 22, 22, 1, 57, 57] 567
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: 1503
number of broken/clashed sets: 56
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071343 none CCC(CO)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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
567  conformations in input
total number of sets (complete confs): 567
using faster count positions algorithm for large data
unique positions, atoms: [27, 19, 6, 19, 54, 1, 6, 1, 1, 1, 1, 7, 7, 31, 31, 57, 57, 57, 57, 57, 1, 31, 31, 31, 31, 31, 19, 54, 54, 162, 1, 1, 1, 7, 7, 7, 57, 1, 1] 567
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 568
number of broken/clashed sets: 56
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071343 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071343
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071343/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071343
Building REAL250005071344
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071344'
/scratch/stefan/7916153/working/building/REAL250005071344 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071344

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071344/0 /scratch/stefan/7916153/working/building/REAL250005071344 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 473)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/473
`/scratch/stefan/7916153/working/3D/473' -> `0.mol2'
Preparing input files

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

`REAL250005071344.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071344.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071344/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071344 none CC(CO)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 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
453  conformations in input
total number of sets (complete confs): 453
using faster count positions algorithm for large data
unique positions, atoms: [150, 96, 150, 151, 66, 96, 66, 66, 22, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 66, 150, 150, 150, 150, 151, 151, 453, 66, 66, 66, 22, 22, 22, 1, 66, 66] 453
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: 1022
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071344 none CC(CO)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 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
453  conformations in input
total number of sets (complete confs): 453
using faster count positions algorithm for large data
unique positions, atoms: [18, 6, 18, 42, 1, 6, 1, 1, 1, 1, 7, 7, 32, 32, 66, 66, 66, 66, 66, 1, 18, 18, 18, 18, 42, 42, 126, 1, 1, 1, 7, 7, 7, 66, 1, 1] 453
rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 19, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 415
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071344 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071344
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071344/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071344
Building REAL250005071345
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071345'
/scratch/stefan/7916153/working/building/REAL250005071345 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071345

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071345/0 /scratch/stefan/7916153/working/building/REAL250005071345 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 474)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/474
`/scratch/stefan/7916153/working/3D/474' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CON=C2)C1)

`REAL250005071345.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071345.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071345/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071345 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CON=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 17, 17, 33, 33, 33, 33, 33, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 1, 6, 6, 6, 33, 1, 1, 1, 26, 26, 1, 1] 100
rigid atoms, others: [1, 10, 11, 12, 13, 20, 25, 26, 27, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29])
total number of confs: 107
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071345 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CON=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 33, 33, 33, 48, 48, 100, 100, 100, 100, 33, 23, 23, 23, 1, 33, 33, 33, 100, 100, 33, 33] 100
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 243
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071345 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CON=C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [58, 25, 58, 85, 85, 100, 100, 100, 100, 100, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 26, 58, 58, 58, 100, 26, 26, 26, 1, 1, 26, 26] 100
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 263
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071345 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071345
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071345/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071345
Building REAL250005071346
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071346'
/scratch/stefan/7916153/working/building/REAL250005071346 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071346

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071346/0 /scratch/stefan/7916153/working/building/REAL250005071346 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 475)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/475
`/scratch/stefan/7916153/working/3D/475' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2C[C@H]2CF)C1)

`REAL250005071346.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071346.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071346/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071346 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2C[C@H]2CF)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
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, 25, 25, 55, 55, 55, 55, 55, 1, 1, 1, 1, 5, 5, 19, 19, 19, 19, 19, 58, 1, 9, 9, 9, 55, 1, 1, 1, 19, 19, 58, 58, 1, 1] 201
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 22, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 320
number of broken/clashed sets: 110
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071346 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2C[C@H]2CF)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 6, 1, 6, 1, 1, 1, 1, 1, 1, 23, 55, 55, 55, 78, 78, 192, 192, 192, 192, 192, 201, 55, 23, 23, 23, 1, 55, 55, 55, 192, 192, 201, 201, 55, 55] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 621
number of broken/clashed sets: 110
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071346 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@@H]2C[C@H]2CF)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 19, 79, 148, 148, 192, 192, 192, 192, 192, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 9, 19, 79, 79, 79, 192, 19, 19, 19, 1, 1, 9, 9, 19, 19] 201
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 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, 32, 33, 34, 35])
total number of confs: 523
number of broken/clashed sets: 110
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071346 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071346
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071346/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071346
Building REAL250005071347
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071347'
/scratch/stefan/7916153/working/building/REAL250005071347 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071347

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071347/0 /scratch/stefan/7916153/working/building/REAL250005071347 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 476)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/476
`/scratch/stefan/7916153/working/3D/476' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)CC1)

`REAL250005071347.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071347.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071347/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071347 none C#CC1(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)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.3', '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']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 6, 1, 6, 1, 1, 1, 1, 10, 10, 35, 35, 63, 63, 63, 63, 63, 1, 17, 17, 17, 1, 1, 1, 11, 11, 11, 63, 1, 1, 17, 17, 17, 17] 141
rigid atoms, others: [3, 5, 6, 7, 8, 18, 22, 23, 24, 29, 30] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 181
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071347 none C#CC1(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)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.3', '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']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 5, 5, 17, 17, 17, 66, 66, 129, 129, 141, 141, 141, 141, 141, 17, 1, 1, 1, 17, 17, 17, 66, 66, 66, 141, 17, 17, 1, 1, 1, 1] 141
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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071347 none C#CC1(C(=O)N2CC(N(C)C(=O)C3=CC(=O)[N-]O3)C2)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.3', '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']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 81, 63, 81, 63, 63, 27, 11, 27, 1, 11, 1, 1, 1, 1, 1, 1, 63, 141, 141, 141, 63, 63, 63, 27, 27, 27, 1, 63, 63, 141, 141, 141, 141] 141
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])
total number of confs: 465
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071347 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071347
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071347/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071347
Building REAL250005071348
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071348'
/scratch/stefan/7916153/working/building/REAL250005071348 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071348

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071348/0 /scratch/stefan/7916153/working/building/REAL250005071348 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 477)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/477
`/scratch/stefan/7916153/working/3D/477' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=COCC2)C1)

`REAL250005071348.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071348.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071348/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071348 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=COCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', '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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 12, 5, 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, 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, 7, 7, 7]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 24, 24, 53, 53, 53, 53, 53, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 1, 9, 9, 9, 53, 1, 1, 1, 34, 34, 34, 34, 34, 1, 1] 140
rigid atoms, others: [1, 34, 33, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32])
total number of confs: 150
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071348 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=COCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', '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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 12, 5, 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, 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, 7, 7, 7]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 53, 53, 53, 82, 82, 140, 140, 140, 140, 53, 27, 27, 27, 1, 53, 53, 53, 140, 140, 140, 140, 140, 53, 53] 140
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 352
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071348 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=COCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', '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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 12, 5, 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, 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, 7, 7, 7]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [87, 33, 87, 131, 131, 140, 140, 140, 140, 140, 34, 34, 12, 1, 12, 1, 1, 1, 1, 1, 34, 87, 87, 87, 140, 34, 34, 34, 1, 1, 1, 1, 1, 34, 34] 140
rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34])
total number of confs: 371
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071348 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071348
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071348/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071348
Building REAL250005071349
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071349'
/scratch/stefan/7916153/working/building/REAL250005071349 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071349

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071349/0 /scratch/stefan/7916153/working/building/REAL250005071349 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 478)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/478
`/scratch/stefan/7916153/working/3D/478' -> `0.mol2'
Preparing input files

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

`REAL250005071349.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071349.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071349/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071349 none C[C@H](O)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
408  conformations in input
total number of sets (complete confs): 408
using faster count positions algorithm for large data
unique positions, atoms: [136, 74, 136, 136, 58, 74, 58, 58, 26, 10, 26, 1, 10, 1, 1, 1, 1, 1, 1, 58, 136, 136, 136, 408, 58, 58, 58, 26, 26, 26, 1, 58, 58] 408
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: 943
number of broken/clashed sets: 61
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071349 none C[C@H](O)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
408  conformations in input
total number of sets (complete confs): 408
using faster count positions algorithm for large data
unique positions, atoms: [22, 6, 22, 22, 1, 6, 1, 1, 1, 1, 10, 10, 33, 33, 58, 58, 58, 58, 58, 1, 22, 22, 22, 66, 1, 1, 1, 11, 11, 11, 58, 1, 1] 408
rigid atoms, others: [32, 4, 6, 7, 8, 9, 19, 24, 25, 26, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 260
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071349 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071349
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071349/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071349
Building REAL250005071350
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071350'
/scratch/stefan/7916153/working/building/REAL250005071350 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071350

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071350/0 /scratch/stefan/7916153/working/building/REAL250005071350 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 479)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/479
`/scratch/stefan/7916153/working/3D/479' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2C=CCC2)C1)

`REAL250005071350.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071350.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071350/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071350 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2C=CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', '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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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, 7]
0  hydrogens need rotated
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 24, 24, 61, 61, 61, 61, 61, 1, 1, 1, 1, 5, 5, 23, 23, 23, 23, 1, 9, 9, 9, 61, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 1, 1] 165
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 175
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071350 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2C=CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', '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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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, 7]
0  hydrogens need rotated
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [36, 10, 1, 10, 1, 1, 1, 1, 1, 1, 36, 61, 61, 61, 81, 81, 165, 165, 165, 165, 61, 36, 36, 36, 1, 61, 61, 61, 165, 165, 165, 165, 165, 165, 165, 61, 61] 165
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 511
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071350 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2C=CCC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', '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: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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, 7]
0  hydrogens need rotated
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [87, 23, 87, 142, 142, 165, 165, 165, 165, 165, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 23, 87, 87, 87, 165, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 23, 23] 165
rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36])
total number of confs: 425
number of broken/clashed sets: 37
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071350 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071350
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071350/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071350
Building REAL250005071351
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071351'
/scratch/stefan/7916153/working/building/REAL250005071351 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071351

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071351/0 /scratch/stefan/7916153/working/building/REAL250005071351 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 480)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/480
`/scratch/stefan/7916153/working/3D/480' -> `0.mol2'
Preparing input files

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

`REAL250005071351.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071351.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071351/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071351 none CC(O)C(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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
456  conformations in input
total number of sets (complete confs): 456
using faster count positions algorithm for large data
unique positions, atoms: [144, 128, 152, 73, 128, 51, 73, 51, 51, 23, 8, 23, 1, 8, 1, 1, 1, 1, 1, 1, 51, 152, 152, 152, 152, 456, 128, 128, 128, 128, 51, 51, 51, 23, 23, 23, 1, 51, 51] 456
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: 1118
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071351 none CC(O)C(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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
456  conformations in input
total number of sets (complete confs): 456
using faster count positions algorithm for large data
unique positions, atoms: [35, 19, 39, 7, 19, 1, 7, 1, 1, 1, 1, 7, 7, 29, 29, 51, 51, 51, 51, 51, 1, 39, 39, 39, 39, 117, 19, 19, 19, 19, 1, 1, 1, 7, 7, 7, 51, 1, 1] 456
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 395
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071351 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071351
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071351/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071351
Building REAL250005071352
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071352'
/scratch/stefan/7916153/working/building/REAL250005071352 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071352

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071352/0 /scratch/stefan/7916153/working/building/REAL250005071352 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 481)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/481
`/scratch/stefan/7916153/working/3D/481' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071352.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071352.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071352/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071352 none C=C1CC1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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: [27, 27, 27, 7, 1, 7, 1, 1, 1, 1, 11, 11, 40, 40, 80, 80, 80, 80, 80, 1, 27, 27, 27, 27, 27, 1, 1, 1, 11, 11, 11, 80, 1, 1] 201
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 19, 25, 26, 27] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 224
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071352 none C=C1CC1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 11, 11, 27, 27, 27, 102, 102, 181, 181, 201, 201, 201, 201, 201, 27, 1, 1, 1, 1, 1, 27, 27, 27, 102, 102, 102, 201, 27, 27] 201
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: 520
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071352 none C=C1CC1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 112, 80, 112, 80, 80, 32, 10, 32, 1, 10, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 201, 80, 80, 80, 32, 32, 32, 1, 80, 80] 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])
total number of confs: 631
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071352 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071352
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071352/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071352
Building REAL250005071353
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071353'
/scratch/stefan/7916153/working/building/REAL250005071353 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071353

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071353/0 /scratch/stefan/7916153/working/building/REAL250005071353 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 482)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/482
`/scratch/stefan/7916153/working/3D/482' -> `0.mol2'
Preparing input files

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

`REAL250005071353.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071353.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071353/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071353 none CC(CF)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [142, 89, 142, 146, 58, 89, 58, 58, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 58, 142, 142, 142, 142, 146, 146, 58, 58, 58, 21, 21, 21, 1, 58, 58] 146
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: 559
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071353 none CC(CF)C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [21, 7, 21, 46, 1, 7, 1, 1, 1, 1, 7, 7, 30, 30, 58, 58, 58, 58, 58, 1, 21, 21, 21, 21, 46, 46, 1, 1, 1, 7, 7, 7, 58, 1, 1] 146
rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 19, 26, 27, 28] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32])
total number of confs: 284
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071353 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071353
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071353/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071353
Building REAL250005071354
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071354'
/scratch/stefan/7916153/working/building/REAL250005071354 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071354

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071354/0 /scratch/stefan/7916153/working/building/REAL250005071354 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 483)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/483
`/scratch/stefan/7916153/working/3D/483' -> `0.mol2'
Preparing input files

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

`REAL250005071354.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071354.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071354/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071354 none C=C(C)CC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 82, 59, 82, 59, 59, 23, 9, 23, 1, 9, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 201, 201, 59, 59, 59, 23, 23, 23, 1, 59, 59] 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: 779
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071354 none C=C(C)CC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 39, 4, 1, 4, 1, 1, 1, 1, 10, 10, 35, 35, 59, 59, 59, 59, 59, 1, 39, 39, 39, 39, 39, 20, 20, 1, 1, 1, 10, 10, 10, 59, 1, 1] 201
rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 19, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 251
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071354 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071354
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071354/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071354
Building REAL250005071355
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071355'
/scratch/stefan/7916153/working/building/REAL250005071355 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071355

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071355/0 /scratch/stefan/7916153/working/building/REAL250005071355 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 484)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/484
`/scratch/stefan/7916153/working/3D/484' -> `0.mol2'
Preparing input files

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

`REAL250005071355.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071355.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071355/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071355 none CCSCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 133, 51, 38, 51, 38, 38, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 38, 201, 201, 201, 201, 201, 133, 133, 38, 38, 38, 16, 16, 16, 1, 38, 38] 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: 666
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071355 none CCSCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 59, 16, 3, 1, 3, 1, 1, 1, 1, 9, 9, 26, 26, 38, 38, 38, 38, 38, 1, 90, 90, 90, 90, 90, 16, 16, 1, 1, 1, 9, 9, 9, 38, 1, 1] 201
rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 19, 27, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 368
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071355 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071355
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071355/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071355
Building REAL250005071356
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071356'
/scratch/stefan/7916153/working/building/REAL250005071356 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071356

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071356/0 /scratch/stefan/7916153/working/building/REAL250005071356 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 485)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/485
`/scratch/stefan/7916153/working/3D/485' -> `0.mol2'
Preparing input files

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

`REAL250005071356.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071356.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071356/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071356 none CC(C)=C(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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, 5, 1, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 196, 196, 136, 196, 99, 136, 99, 99, 38, 12, 38, 1, 12, 1, 1, 1, 1, 1, 1, 99, 196, 196, 196, 196, 196, 196, 196, 196, 196, 99, 99, 99, 38, 38, 38, 1, 99, 99] 196
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: 635
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071356 none CC(C)=C(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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, 5, 1, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 7, 23, 1, 7, 1, 1, 1, 1, 11, 11, 40, 40, 99, 99, 99, 99, 99, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 11, 11, 11, 99, 1, 1] 196
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 241
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071356 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071356
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071356/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071356
Building REAL250005071357
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071357'
/scratch/stefan/7916153/working/building/REAL250005071357 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071357

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071357/0 /scratch/stefan/7916153/working/building/REAL250005071357 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 486)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/486
`/scratch/stefan/7916153/working/3D/486' -> `0.mol2'
Preparing input files

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

`REAL250005071357.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071357.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071357/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071357 none CCCC(O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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, 197, 148, 65, 148, 46, 65, 46, 46, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 46, 201, 201, 201, 201, 201, 197, 197, 148, 444, 46, 46, 46, 21, 21, 21, 1, 46, 46] 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: 1303
number of broken/clashed sets: 51
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071357 none CCCC(O)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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: [57, 49, 18, 6, 18, 1, 6, 1, 1, 1, 1, 9, 9, 26, 26, 46, 46, 46, 46, 46, 1, 57, 57, 57, 57, 55, 52, 52, 18, 54, 1, 1, 1, 9, 9, 9, 46, 1, 1] 603
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 395
number of broken/clashed sets: 51
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071357 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071357
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071357/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071357
Building REAL250005071358
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071358'
/scratch/stefan/7916153/working/building/REAL250005071358 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071358

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071358/0 /scratch/stefan/7916153/working/building/REAL250005071358 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 487)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/487
`/scratch/stefan/7916153/working/3D/487' -> `0.mol2'
Preparing input files

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

`REAL250005071358.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071358.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071358/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071358 none CCC(O)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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, 198, 168, 198, 58, 43, 58, 43, 43, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 43, 201, 201, 201, 201, 201, 198, 594, 168, 168, 43, 43, 43, 20, 20, 20, 1, 43, 43] 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: 1395
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071358 none CCC(O)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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: [61, 43, 19, 43, 5, 1, 5, 1, 1, 1, 1, 9, 9, 28, 28, 43, 43, 43, 43, 43, 1, 61, 61, 61, 61, 61, 43, 129, 19, 19, 1, 1, 1, 9, 9, 9, 43, 1, 1] 603
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 496
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071358 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071358
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071358/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071358
Building REAL250005071359
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071359'
/scratch/stefan/7916153/working/building/REAL250005071359 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071359

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071359/0 /scratch/stefan/7916153/working/building/REAL250005071359 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 488)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/488
`/scratch/stefan/7916153/working/3D/488' -> `0.mol2'
Preparing input files

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

`REAL250005071359.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071359.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071359/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071359 none CC(Cl)=CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 1, 16, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 201, 120, 83, 120, 83, 83, 32, 11, 32, 1, 11, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 201, 83, 83, 83, 32, 32, 32, 1, 83, 83] 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: 635
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071359 none CC(Cl)=CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 1, 16, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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: [24, 24, 23, 7, 1, 7, 1, 1, 1, 1, 11, 11, 42, 42, 83, 83, 83, 83, 83, 1, 24, 24, 24, 24, 1, 1, 1, 11, 11, 11, 83, 1, 1] 201
rigid atoms, others: [32, 4, 6, 7, 8, 9, 19, 24, 25, 26, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 226
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071359 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071359
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071359/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071359
Building REAL250005071360
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071360'
/scratch/stefan/7916153/working/building/REAL250005071360 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071360

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071360/0 /scratch/stefan/7916153/working/building/REAL250005071360 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 489)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/489
`/scratch/stefan/7916153/working/3D/489' -> `0.mol2'
Preparing input files

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

`REAL250005071360.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071360.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071360/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071360 none CC=CC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 104, 73, 104, 73, 73, 28, 11, 28, 1, 11, 1, 1, 1, 1, 1, 1, 73, 137, 137, 137, 137, 137, 73, 73, 73, 28, 28, 28, 1, 73, 73] 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: 437
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071360 none CC=CC(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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: [20, 20, 6, 1, 6, 1, 1, 1, 1, 11, 11, 37, 37, 73, 73, 73, 73, 73, 1, 20, 20, 20, 19, 20, 1, 1, 1, 11, 11, 11, 73, 1, 1] 137
rigid atoms, others: [32, 3, 5, 6, 7, 8, 18, 24, 25, 26, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 27, 28, 29, 30])
total number of confs: 198
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071360 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071360
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071360/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071360
Building REAL250005071361
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071361'
/scratch/stefan/7916153/working/building/REAL250005071361 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071361

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071361/0 /scratch/stefan/7916153/working/building/REAL250005071361 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 490)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/490
`/scratch/stefan/7916153/working/3D/490' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)CC2F)C1)

`REAL250005071361.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071361.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071361/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071361 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)CC2F)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 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, 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
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 22, 22, 40, 40, 40, 40, 40, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 1, 9, 9, 9, 40, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1] 84
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33])
total number of confs: 107
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071361 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)CC2F)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 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, 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
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 40, 40, 40, 55, 55, 84, 84, 84, 84, 40, 23, 23, 23, 1, 40, 40, 40, 84, 84, 84, 84, 84, 84, 40, 40] 84
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 289
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071361 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(C)CC2F)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 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, 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
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [33, 9, 33, 63, 63, 84, 84, 84, 84, 84, 9, 9, 3, 1, 3, 1, 1, 1, 1, 1, 9, 33, 33, 33, 84, 9, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9] 84
rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35])
total number of confs: 207
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071361 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071361
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071361/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071361
Building REAL250005071362
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071362'
/scratch/stefan/7916153/working/building/REAL250005071362 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071362

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071362/0 /scratch/stefan/7916153/working/building/REAL250005071362 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 491)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/491
`/scratch/stefan/7916153/working/3D/491' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2C[C@@H](O)C2)C1)

`REAL250005071362.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071362.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071362/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071362 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2C[C@@H](O)C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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]
1  hydrogens need rotated
522  conformations in input
total number of sets (complete confs): 522
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 20, 20, 57, 57, 57, 57, 57, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 29, 1, 8, 8, 8, 57, 1, 1, 1, 29, 29, 87, 29, 29, 1, 1] 522
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 22, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33, 34])
total number of confs: 261
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071362 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2C[C@@H](O)C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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]
1  hydrogens need rotated
522  conformations in input
total number of sets (complete confs): 522
using faster count positions algorithm for large data
unique positions, atoms: [36, 10, 1, 10, 1, 1, 1, 1, 1, 1, 36, 57, 57, 57, 83, 83, 174, 174, 174, 174, 174, 174, 57, 36, 36, 36, 1, 57, 57, 57, 174, 174, 522, 174, 174, 57, 57] 522
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 1073
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071362 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H]2C[C@@H](O)C2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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]
1  hydrogens need rotated
522  conformations in input
total number of sets (complete confs): 522
using faster count positions algorithm for large data
unique positions, atoms: [89, 29, 89, 138, 138, 174, 174, 174, 174, 174, 29, 29, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 29, 89, 89, 89, 174, 29, 29, 29, 1, 1, 6, 1, 1, 29, 29] 522
rigid atoms, others: [33, 34, 13, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36])
total number of confs: 435
number of broken/clashed sets: 48
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071362 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071362
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071362/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071362
Building REAL250005071363
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071363'
/scratch/stefan/7916153/working/building/REAL250005071363 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071363

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071363/0 /scratch/stefan/7916153/working/building/REAL250005071363 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 492)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/492
`/scratch/stefan/7916153/working/3D/492' -> `0.mol2'
Preparing input files

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

`REAL250005071363.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071363.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071363/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071363 none C[C@@H]1C[C@H]1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 32, 6, 32, 1, 6, 1, 1, 1, 1, 7, 7, 34, 34, 75, 75, 75, 75, 75, 1, 32, 32, 32, 32, 32, 1, 1, 1, 7, 7, 7, 75, 1, 1] 171
rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 220
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071363 none C[C@@H]1C[C@H]1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 32, 32, 32, 85, 85, 161, 161, 171, 171, 171, 171, 171, 32, 2, 2, 2, 1, 1, 32, 32, 32, 85, 85, 85, 171, 32, 32] 171
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: 448
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071363 none C[C@@H]1C[C@H]1C(=O)N1CC(N(C)C(=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', 'N.am', 'C.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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [171, 171, 171, 171, 110, 171, 75, 110, 75, 75, 25, 9, 25, 1, 9, 1, 1, 1, 1, 1, 1, 75, 171, 171, 171, 171, 171, 75, 75, 75, 25, 25, 25, 1, 75, 75] 171
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: 541
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071363 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071363
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071363/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071363
Building REAL250005071364
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071364'
/scratch/stefan/7916153/working/building/REAL250005071364 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071364

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071364/0 /scratch/stefan/7916153/working/building/REAL250005071364 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 493)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/493
`/scratch/stefan/7916153/working/3D/493' -> `0.mol2'
Preparing input files

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

`REAL250005071364.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071364.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071364/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071364 none CNC(=O)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 5, 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, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 191, 201, 80, 49, 80, 49, 49, 18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 49, 201, 201, 201, 201, 191, 191, 49, 49, 49, 18, 18, 18, 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: 778
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071364 none CNC(=O)CC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 5, 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, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 17, 52, 3, 1, 3, 1, 1, 1, 1, 10, 10, 34, 34, 49, 49, 49, 49, 49, 1, 52, 52, 52, 52, 17, 17, 1, 1, 1, 10, 10, 10, 49, 1, 1] 201
rigid atoms, others: [34, 35, 5, 7, 8, 9, 10, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 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
/scratch/stefan/7916153/working/building/REAL250005071364 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071364
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071364/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071364
Building REAL250005071365
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071365'
/scratch/stefan/7916153/working/building/REAL250005071365 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071365

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071365/0 /scratch/stefan/7916153/working/building/REAL250005071365 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 494)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/494
`/scratch/stefan/7916153/working/3D/494' -> `0.mol2'
Preparing input files

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

`REAL250005071365.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071365.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071365/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071365 none C=CC=CCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 63, 45, 63, 45, 45, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 45, 201, 201, 201, 201, 201, 163, 163, 45, 45, 45, 20, 20, 20, 1, 45, 45] 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: 792
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071365 none C=CC=CCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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']
dock atom type numbers: [1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 3, 1, 3, 1, 1, 1, 1, 8, 8, 28, 28, 45, 45, 45, 45, 45, 1, 44, 44, 44, 44, 44, 16, 16, 1, 1, 1, 8, 8, 8, 45, 1, 1] 201
rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 230
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071365 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071365
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071365/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071365
Building REAL250005071366
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071366'
/scratch/stefan/7916153/working/building/REAL250005071366 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071366

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071366/0 /scratch/stefan/7916153/working/building/REAL250005071366 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 495)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/495
`/scratch/stefan/7916153/working/3D/495' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCC(N)=O)C1)

`REAL250005071366.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071366.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071366/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071366 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCC(N)=O)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', '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, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 4, 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: [9, 1, 9, 22, 22, 41, 41, 41, 41, 41, 1, 1, 1, 1, 4, 4, 23, 40, 88, 88, 1, 9, 9, 9, 41, 1, 1, 1, 23, 23, 40, 40, 88, 88, 1, 1] 201
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33])
total number of confs: 402
number of broken/clashed sets: 138
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071366 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)CCC(N)=O)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', '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, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 4, 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: [21, 6, 1, 6, 1, 1, 1, 1, 1, 1, 21, 41, 41, 41, 63, 63, 155, 186, 201, 201, 41, 21, 21, 21, 1, 41, 41, 41, 155, 155, 186, 186, 201, 201, 41, 41] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 816
number of broken/clashed sets: 138
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071366 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071366
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071366/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071366
Building REAL250005071367
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071367'
/scratch/stefan/7916153/working/building/REAL250005071367 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071367

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071367/0 /scratch/stefan/7916153/working/building/REAL250005071367 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 496)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/496
`/scratch/stefan/7916153/working/3D/496' -> `0.mol2'
Preparing input files

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

`REAL250005071367.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071367.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071367/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071367 none CC(O)CCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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: [90, 90, 90, 88, 45, 34, 45, 34, 34, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 34, 90, 90, 90, 90, 270, 90, 90, 88, 88, 34, 34, 34, 14, 14, 14, 1, 34, 34] 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: 627
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071367 none CC(O)CCC(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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: [18, 16, 18, 14, 2, 1, 2, 1, 1, 1, 1, 8, 8, 20, 20, 34, 34, 34, 34, 34, 1, 18, 18, 18, 18, 54, 16, 16, 14, 14, 1, 1, 1, 8, 8, 8, 34, 1, 1] 270
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 203
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071367 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071367
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071367/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071367
Building REAL250005071368
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071368'
/scratch/stefan/7916153/working/building/REAL250005071368 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071368

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071368/0 /scratch/stefan/7916153/working/building/REAL250005071368 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 497)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/497
`/scratch/stefan/7916153/working/3D/497' -> `0.mol2'
Preparing input files

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

`REAL250005071368.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071368.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071368/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071368 none C#CCC(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 81, 52, 81, 32, 52, 32, 32, 12, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 32, 98, 98, 98, 81, 81, 81, 81, 32, 32, 32, 12, 12, 12, 1, 32, 32] 98
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: 412
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071368 none C#CCC(C)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 25, 13, 5, 13, 1, 5, 1, 1, 1, 1, 8, 8, 20, 20, 32, 32, 32, 32, 32, 1, 25, 25, 25, 13, 13, 13, 13, 1, 1, 1, 8, 8, 8, 32, 1, 1] 98
rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34])
total number of confs: 174
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071368 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071368
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071368/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071368
Building REAL250005071369
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071369'
/scratch/stefan/7916153/working/building/REAL250005071369 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071369

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071369/0 /scratch/stefan/7916153/working/building/REAL250005071369 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 498)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/498
`/scratch/stefan/7916153/working/3D/498' -> `0.mol2'
Preparing input files

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

`REAL250005071369.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071369.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071369/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071369 none CC(CCO)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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: [164, 109, 164, 198, 201, 69, 109, 69, 69, 24, 8, 24, 1, 8, 1, 1, 1, 1, 1, 1, 69, 164, 164, 164, 164, 201, 201, 201, 198, 603, 69, 69, 69, 24, 24, 24, 1, 69, 69] 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: 1403
number of broken/clashed sets: 77
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071369 none CC(CCO)C(=O)N1CC(N(C)C(=O)C2=CC(=O)[N-]O2)C1 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.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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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: [17, 6, 17, 36, 63, 1, 6, 1, 1, 1, 1, 9, 9, 33, 33, 69, 69, 69, 69, 69, 1, 18, 18, 18, 17, 39, 39, 63, 60, 189, 1, 1, 1, 9, 9, 9, 69, 1, 1] 603
rigid atoms, others: [32, 5, 38, 7, 8, 9, 10, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36])
total number of confs: 630
number of broken/clashed sets: 77
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071369 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071369
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071369/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071369
Building REAL250005071370
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071370'
/scratch/stefan/7916153/working/building/REAL250005071370 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071370

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071370/0 /scratch/stefan/7916153/working/building/REAL250005071370 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 499)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/499
`/scratch/stefan/7916153/working/3D/499' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H](O)CF)C1)

`REAL250005071370.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071370.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071370/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071370 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H](O)CF)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
1  hydrogens need rotated
570  conformations in input
total number of sets (complete confs): 570
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 23, 23, 61, 61, 61, 61, 61, 1, 1, 1, 1, 7, 7, 26, 26, 26, 63, 1, 9, 9, 9, 61, 1, 1, 1, 78, 63, 63, 1, 1] 570
rigid atoms, others: [32, 1, 10, 11, 12, 13, 20, 25, 26, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30])
total number of confs: 416
number of broken/clashed sets: 110
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071370 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)[C@H](O)CF)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 12, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
1  hydrogens need rotated
570  conformations in input
total number of sets (complete confs): 570
using faster count positions algorithm for large data
unique positions, atoms: [33, 9, 1, 9, 1, 1, 1, 1, 1, 1, 33, 61, 61, 61, 92, 92, 180, 180, 180, 190, 61, 33, 33, 33, 1, 61, 61, 61, 540, 190, 190, 61, 61] 570
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 1279
number of broken/clashed sets: 110
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071370 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071370
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071370/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071370
Building REAL250005071371
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071371'
/scratch/stefan/7916153/working/building/REAL250005071371 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071371

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071371/0 /scratch/stefan/7916153/working/building/REAL250005071371 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 500)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/500
`/scratch/stefan/7916153/working/3D/500' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(O)CC2)C1)

`REAL250005071371.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071371.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071371/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071371 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(O)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 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, 3, 7, 3, 7, 7, 7, 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
492  conformations in input
total number of sets (complete confs): 492
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 24, 24, 69, 69, 69, 69, 69, 1, 1, 1, 1, 7, 7, 25, 25, 25, 1, 9, 9, 9, 69, 1, 1, 1, 75, 25, 25, 25, 25, 1, 1] 492
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 19, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 27, 28, 29, 30, 31])
total number of confs: 262
number of broken/clashed sets: 120
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071371 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(O)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 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, 3, 7, 3, 7, 7, 7, 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
492  conformations in input
total number of sets (complete confs): 492
using faster count positions algorithm for large data
unique positions, atoms: [34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 69, 69, 69, 102, 102, 164, 164, 164, 69, 34, 34, 34, 1, 69, 69, 69, 492, 164, 164, 164, 164, 69, 69] 492
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 1015
number of broken/clashed sets: 120
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071371 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2(O)CC2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 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, 3, 7, 3, 7, 7, 7, 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
492  conformations in input
total number of sets (complete confs): 492
using faster count positions algorithm for large data
unique positions, atoms: [84, 25, 84, 144, 144, 164, 164, 164, 164, 164, 25, 25, 9, 1, 9, 1, 1, 1, 1, 25, 84, 84, 84, 164, 25, 25, 25, 6, 1, 1, 1, 1, 25, 25] 492
rigid atoms, others: [13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 440
number of broken/clashed sets: 120
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071371 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071371
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071371/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071371
Building REAL250005071372
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071372'
/scratch/stefan/7916153/working/building/REAL250005071372 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071372

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071372/0 /scratch/stefan/7916153/working/building/REAL250005071372 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 501)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/501
`/scratch/stefan/7916153/working/3D/501' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071372.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071372.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071372/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071372 none CN(C(=O)CC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 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]
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]
0  hydrogens 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, 32, 32, 99, 132, 132, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 9, 9, 9, 99, 99, 132, 132, 132, 132, 132, 1, 1, 1, 21, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 8, 9, 10, 11, 19, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 515
number of broken/clashed sets: 94
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071372 none CN(C(=O)CC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 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]
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]
0  hydrogens 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, 17, 3, 17, 1, 1, 1, 1, 56, 132, 132, 132, 193, 193, 201, 201, 201, 201, 201, 132, 56, 56, 56, 3, 3, 1, 1, 1, 1, 1, 132, 132, 132, 201, 132, 132] 201
rigid atoms, others: [4, 5, 6, 7, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35])
total number of confs: 608
number of broken/clashed sets: 94
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071372 none CN(C(=O)CC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 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]
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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 21, 66, 120, 120, 177, 201, 201, 21, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 66, 66, 66, 177, 177, 201, 201, 201, 201, 201, 21, 20, 21, 1, 21, 21] 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: 734
number of broken/clashed sets: 94
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071372 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071372
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071372/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071372
Building REAL250005071373
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071373'
/scratch/stefan/7916153/working/building/REAL250005071373 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071373

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071373/0 /scratch/stefan/7916153/working/building/REAL250005071373 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 502)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/502
`/scratch/stefan/7916153/working/3D/502' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C(C)(C)F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071373.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071373.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071373/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071373 none CN(C(=O)C(C)(C)F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', '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, 5, 5, 15, 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]
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]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [74, 26, 74, 108, 108, 123, 123, 123, 26, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 74, 74, 74, 123, 123, 123, 123, 123, 123, 26, 25, 25, 1, 26, 25] 123
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: 374
number of broken/clashed sets: 54
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071373 none CN(C(=O)C(C)(C)F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', '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, 5, 5, 15, 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]
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]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 32, 32, 56, 56, 56, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 9, 9, 9, 56, 56, 56, 56, 56, 56, 1, 1, 1, 25, 1, 1] 123
rigid atoms, others: [1, 34, 33, 8, 9, 10, 11, 19, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 240
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071373 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071373
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071373/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071373
Building REAL250005071374
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071374'
/scratch/stefan/7916153/working/building/REAL250005071374 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071374

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071374/0 /scratch/stefan/7916153/working/building/REAL250005071374 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 503)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/503
`/scratch/stefan/7916153/working/3D/503' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C(C)(F)F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071374.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071374.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071374/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071374 none CN(C(=O)C(C)(F)F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 5, 5, 15, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [65, 27, 65, 84, 84, 100, 100, 100, 27, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 65, 65, 65, 100, 100, 100, 27, 26, 27, 1, 27, 27] 100
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: 303
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071374 none CN(C(=O)C(C)(F)F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 5, 5, 15, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 26, 26, 53, 53, 53, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 9, 9, 9, 53, 53, 53, 1, 1, 1, 27, 1, 1] 100
rigid atoms, others: [1, 8, 9, 10, 11, 19, 26, 27, 28, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 29])
total number of confs: 230
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071374 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071374
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071374/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071374
Building REAL250005071375
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071375'
/scratch/stefan/7916153/working/building/REAL250005071375 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071375

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071375/0 /scratch/stefan/7916153/working/building/REAL250005071375 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 504)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/504
`/scratch/stefan/7916153/working/3D/504' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071375.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071375.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071375/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071375 none COCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
195  conformations in input
total number of sets (complete confs): 195
using faster count positions algorithm for large data
unique positions, atoms: [195, 189, 119, 80, 119, 23, 80, 23, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 195, 195, 195, 189, 189, 80, 80, 80, 23, 22, 23, 1, 23, 23] 195
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: 683
number of broken/clashed sets: 87
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071375 none COCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [126, 72, 26, 9, 26, 1, 9, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 126, 126, 126, 72, 72, 9, 9, 9, 1, 1, 1, 23, 1, 1] 195
rigid atoms, others: [32, 5, 7, 8, 9, 10, 18, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 380
number of broken/clashed sets: 87
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071375 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071375
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071375/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071375
Building REAL250005071376
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071376'
/scratch/stefan/7916153/working/building/REAL250005071376 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071376

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071376/0 /scratch/stefan/7916153/working/building/REAL250005071376 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 505)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/505
`/scratch/stefan/7916153/working/3D/505' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071376.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071376.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071376/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071376 none CCCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 132, 75, 132, 23, 75, 23, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 201, 201, 201, 201, 201, 198, 198, 75, 75, 75, 23, 22, 23, 1, 23, 23] 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: 697
number of broken/clashed sets: 91
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071376 none CCCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 93, 29, 9, 29, 1, 9, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 119, 119, 119, 119, 119, 93, 93, 9, 9, 9, 1, 1, 1, 23, 1, 1] 201
rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 590
number of broken/clashed sets: 91
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071376 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071376
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071376/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071376
Building REAL250005071377
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071377'
/scratch/stefan/7916153/working/building/REAL250005071377 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071377

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071377/0 /scratch/stefan/7916153/working/building/REAL250005071377 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 506)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/506
`/scratch/stefan/7916153/working/3D/506' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC=CO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071377.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071377.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071377/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071377 none CN(C(=O)C1=CC=CO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 29, 29, 71, 71, 71, 71, 1, 1, 1, 1, 6, 6, 23, 23, 24, 23, 23, 1, 9, 9, 9, 71, 71, 71, 1, 1, 1, 24, 1, 1] 129
rigid atoms, others: [32, 1, 9, 10, 11, 12, 20, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 165
number of broken/clashed sets: 63
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071377 none CN(C(=O)C1=CC=CO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [33, 10, 1, 10, 1, 1, 1, 1, 1, 33, 71, 71, 71, 124, 124, 129, 129, 129, 129, 129, 70, 33, 33, 33, 1, 1, 1, 71, 71, 71, 129, 71, 71] 129
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32])
total number of confs: 398
number of broken/clashed sets: 63
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071377 none CN(C(=O)C1=CC=CO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [80, 24, 80, 113, 113, 129, 129, 129, 129, 24, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 80, 80, 80, 129, 129, 129, 24, 23, 23, 1, 24, 23] 129
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: 325
number of broken/clashed sets: 63
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071377 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071377
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071377/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071377
Building REAL250005071378
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071378'
/scratch/stefan/7916153/working/building/REAL250005071378 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071378

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071378/0 /scratch/stefan/7916153/working/building/REAL250005071378 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 507)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/507
`/scratch/stefan/7916153/working/3D/507' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071378.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071378.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071378/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071378 none CC(=O)NCC(=O)N(C)C1CN(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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [140, 140, 140, 126, 59, 38, 59, 11, 38, 11, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 140, 140, 140, 140, 126, 126, 38, 38, 38, 11, 10, 11, 1, 11, 11] 140
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: 504
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071378 none CC(=O)NCC(=O)N(C)C1CN(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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 104, 69, 20, 9, 20, 1, 9, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 1, 104, 104, 104, 104, 69, 69, 9, 9, 9, 1, 1, 1, 11, 1, 1] 140
rigid atoms, others: [32, 34, 35, 7, 9, 10, 11, 12, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 382
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071378 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071378
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071378/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071378
Building REAL250005071379
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071379'
/scratch/stefan/7916153/working/building/REAL250005071379 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071379

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071379/0 /scratch/stefan/7916153/working/building/REAL250005071379 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 508)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/508
`/scratch/stefan/7916153/working/3D/508' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071379.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071379.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071379/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071379 none CC(C)CC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [147, 146, 148, 116, 78, 116, 28, 78, 28, 27, 11, 1, 11, 1, 1, 1, 1, 1, 1, 28, 148, 148, 148, 148, 148, 148, 148, 146, 146, 78, 78, 78, 28, 27, 28, 1, 28, 28] 148
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: 503
number of broken/clashed sets: 70
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071379 none CC(C)CC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [67, 63, 68, 32, 9, 32, 1, 9, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 68, 68, 68, 68, 68, 68, 68, 63, 63, 9, 9, 9, 1, 1, 1, 28, 1, 1] 148
rigid atoms, others: [32, 33, 34, 36, 37, 6, 8, 9, 10, 11, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 313
number of broken/clashed sets: 70
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071379 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071379
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071379/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071379
Building REAL250005071380
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071380'
/scratch/stefan/7916153/working/building/REAL250005071380 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071380

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071380/0 /scratch/stefan/7916153/working/building/REAL250005071380 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 509)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/509
`/scratch/stefan/7916153/working/3D/509' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071380.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071380.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071380/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071380 none CC1CC1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [58, 58, 58, 23, 9, 23, 1, 9, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 58, 58, 58, 58, 58, 58, 58, 9, 9, 9, 1, 1, 1, 23, 1, 1] 108
rigid atoms, others: [32, 34, 35, 6, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 196
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071380 none CC1CC1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 29, 29, 58, 58, 58, 85, 95, 108, 108, 108, 108, 108, 58, 2, 2, 2, 1, 1, 1, 1, 29, 29, 29, 58, 58, 58, 108, 58, 58] 108
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: 307
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071380 none CC1CC1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 108, 81, 52, 81, 23, 52, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 108, 108, 108, 108, 108, 108, 108, 52, 52, 52, 23, 23, 23, 1, 23, 23] 108
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: 325
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071380 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071380
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071380/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071380
Building REAL250005071381
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071381'
/scratch/stefan/7916153/working/building/REAL250005071381 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071381

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071381/0 /scratch/stefan/7916153/working/building/REAL250005071381 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 510)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/510
`/scratch/stefan/7916153/working/3D/510' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071381.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071381.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071381/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071381 none CCOCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 162, 91, 56, 91, 16, 56, 16, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 201, 201, 201, 201, 201, 162, 162, 56, 56, 56, 16, 15, 16, 1, 16, 16] 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: 664
number of broken/clashed sets: 77
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071381 none CCOCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 129, 70, 23, 9, 23, 1, 9, 1, 1, 1, 1, 5, 5, 15, 15, 15, 15, 15, 1, 137, 137, 137, 137, 137, 70, 70, 9, 9, 9, 1, 1, 1, 16, 1, 1] 201
rigid atoms, others: [32, 34, 35, 6, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 423
number of broken/clashed sets: 77
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071381 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071381
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071381/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071381
Building REAL250005071382
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071382'
/scratch/stefan/7916153/working/building/REAL250005071382 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071382

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071382/0 /scratch/stefan/7916153/working/building/REAL250005071382 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 511)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/511
`/scratch/stefan/7916153/working/3D/511' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071382.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071382.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071382/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071382 none CC(C)=CC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 98, 66, 98, 22, 66, 22, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 126, 126, 126, 126, 126, 126, 126, 66, 66, 66, 22, 21, 21, 1, 21, 21] 126
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: 385
number of broken/clashed sets: 54
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071382 none CC(C)=CC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [57, 57, 57, 29, 9, 29, 1, 9, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 57, 57, 57, 57, 57, 57, 57, 9, 9, 9, 1, 1, 1, 21, 1, 1] 126
rigid atoms, others: [32, 34, 35, 6, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 192
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071382 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071382
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071382/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071382
Building REAL250005071383
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071383'
/scratch/stefan/7916153/working/building/REAL250005071383 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071383

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071383/0 /scratch/stefan/7916153/working/building/REAL250005071383 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 512)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/512
`/scratch/stefan/7916153/working/3D/512' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1CCCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071383.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071383.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071383/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071383 none CN(C(=O)C1CCCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 22, 22, 47, 47, 47, 47, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 8, 8, 8, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 23, 1, 1] 97
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 168
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071383 none CN(C(=O)C1CCCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [24, 8, 1, 8, 1, 1, 1, 1, 1, 24, 47, 47, 47, 82, 82, 97, 97, 97, 97, 97, 47, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 97, 47, 47] 97
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36])
total number of confs: 280
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071383 none CN(C(=O)C1CCCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 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
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [52, 24, 52, 81, 81, 97, 97, 97, 97, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 52, 52, 52, 97, 97, 97, 97, 97, 97, 97, 24, 24, 24, 1, 23, 23] 97
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: 293
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071383 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071383
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071383/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071383
Building REAL250005071384
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071384'
/scratch/stefan/7916153/working/building/REAL250005071384 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071384

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071384/0 /scratch/stefan/7916153/working/building/REAL250005071384 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 513)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/513
`/scratch/stefan/7916153/working/3D/513' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071384.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071384.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071384/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071384 none CSCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 107, 70, 107, 19, 70, 19, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 163, 163, 70, 70, 70, 19, 18, 19, 1, 19, 19] 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])
total number of confs: 623
number of broken/clashed sets: 104
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071384 none CSCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 74, 25, 9, 25, 1, 9, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 137, 143, 143, 74, 74, 9, 9, 9, 1, 1, 1, 19, 1, 1] 201
rigid atoms, others: [32, 5, 7, 8, 9, 10, 18, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 413
number of broken/clashed sets: 104
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071384 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071384
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071384/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071384
Building REAL250005071385
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071385'
/scratch/stefan/7916153/working/building/REAL250005071385 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071385

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071385/0 /scratch/stefan/7916153/working/building/REAL250005071385 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 514)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/514
`/scratch/stefan/7916153/working/3D/514' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071385.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071385.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071385/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071385 none CSCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 125, 127, 77, 46, 77, 14, 46, 14, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 127, 127, 127, 127, 46, 46, 46, 14, 13, 14, 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: 576
number of broken/clashed sets: 90
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071385 none CSCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 68, 69, 25, 9, 25, 1, 9, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 1, 149, 149, 149, 70, 70, 69, 69, 9, 9, 9, 1, 1, 1, 14, 1, 1] 201
rigid atoms, others: [32, 34, 35, 6, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 411
number of broken/clashed sets: 90
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071385 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071385
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071385/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071385
Building REAL250005071386
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071386'
/scratch/stefan/7916153/working/building/REAL250005071386 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071386

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071386/0 /scratch/stefan/7916153/working/building/REAL250005071386 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 515)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/515
`/scratch/stefan/7916153/working/3D/515' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071386.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071386.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071386/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071386 none CC(C)CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 191, 201, 178, 99, 53, 99, 18, 53, 18, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 201, 201, 200, 201, 201, 201, 201, 191, 191, 178, 178, 53, 53, 53, 18, 17, 18, 1, 18, 18] 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: 780
number of broken/clashed sets: 88
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071386 none CC(C)CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 118, 139, 99, 29, 9, 29, 1, 9, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 139, 139, 135, 139, 139, 139, 139, 118, 118, 99, 99, 9, 9, 9, 1, 1, 1, 18, 1, 1] 201
rigid atoms, others: [35, 36, 37, 7, 40, 9, 10, 11, 12, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 633
number of broken/clashed sets: 88
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071386 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071386
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071386/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071386
Building REAL250005071387
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071387'
/scratch/stefan/7916153/working/building/REAL250005071387 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071387

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071387/0 /scratch/stefan/7916153/working/building/REAL250005071387 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 516)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/516
`/scratch/stefan/7916153/working/3D/516' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC=CN1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071387.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071387.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071387/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071387 none CN(C(=O)C1=CC=CN1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 1, 1, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 6, 7, 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]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 24, 24, 67, 67, 67, 67, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 7, 7, 7, 67, 67, 67, 67, 1, 1, 1, 28, 1, 1] 135
rigid atoms, others: [32, 1, 33, 9, 10, 11, 12, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 162
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071387 none CN(C(=O)C1=CC=CN1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 1, 1, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 6, 7, 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]
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: [34, 11, 1, 11, 1, 1, 1, 1, 1, 34, 67, 67, 67, 115, 115, 135, 135, 135, 135, 135, 67, 34, 34, 34, 1, 1, 1, 1, 67, 67, 67, 135, 67, 67] 135
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33])
total number of confs: 396
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071387 none CN(C(=O)C1=CC=CN1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 1, 1, 1, 1, 8, 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]
dock color type numbers: [7, 7, 7, 6, 7, 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]
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: [61, 28, 61, 99, 99, 135, 135, 135, 135, 28, 27, 11, 1, 11, 1, 1, 1, 1, 1, 1, 28, 61, 61, 61, 135, 135, 135, 135, 28, 27, 28, 1, 28, 28] 135
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])
total number of confs: 344
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071387 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071387
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071387/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071387
Building REAL250005071388
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071388'
/scratch/stefan/7916153/working/building/REAL250005071388 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071388

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071388/0 /scratch/stefan/7916153/working/building/REAL250005071388 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 517)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/517
`/scratch/stefan/7916153/working/3D/517' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=COC=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071388.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071388.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071388/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071388 none CN(C(=O)C1=COC=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 12, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 7, 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
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 24, 24, 66, 66, 66, 66, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 7, 7, 7, 66, 66, 66, 1, 1, 1, 30, 1, 1] 129
rigid atoms, others: [32, 1, 9, 10, 11, 12, 20, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 164
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071388 none CN(C(=O)C1=COC=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 12, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 7, 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
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [36, 11, 1, 11, 1, 1, 1, 1, 1, 36, 66, 66, 66, 115, 115, 129, 129, 129, 129, 129, 66, 36, 36, 36, 1, 1, 1, 66, 66, 66, 129, 66, 66] 129
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32])
total number of confs: 394
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071388 none CN(C(=O)C1=COC=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 12, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 7, 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
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [57, 30, 57, 99, 99, 129, 129, 129, 129, 30, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 57, 57, 57, 129, 129, 129, 30, 29, 30, 1, 30, 30] 129
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: 325
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071388 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071388
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071388/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071388
Building REAL250005071389
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071389'
/scratch/stefan/7916153/working/building/REAL250005071389 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071389

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071389/0 /scratch/stefan/7916153/working/building/REAL250005071389 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 518)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/518
`/scratch/stefan/7916153/working/3D/518' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071389.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071389.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071389/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071389 none CCCCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 194, 158, 136, 57, 29, 57, 10, 29, 10, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 201, 201, 201, 201, 201, 194, 194, 160, 160, 136, 136, 29, 29, 29, 10, 9, 10, 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: 854
number of broken/clashed sets: 71
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071389 none CCCCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 135, 102, 84, 23, 9, 23, 1, 9, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 1, 156, 157, 157, 157, 157, 135, 135, 105, 105, 84, 84, 9, 9, 9, 1, 1, 1, 10, 1, 1] 201
rigid atoms, others: [35, 36, 37, 7, 40, 9, 10, 11, 12, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 734
number of broken/clashed sets: 71
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071389 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071389
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071389/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071389
Building REAL250005071390
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071390'
/scratch/stefan/7916153/working/building/REAL250005071390 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071390

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071390/0 /scratch/stefan/7916153/working/building/REAL250005071390 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 519)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/519
`/scratch/stefan/7916153/working/3D/519' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CC(C)(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071390.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071390.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071390/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071390 none CN(C(=O)CC(C)(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [82, 28, 82, 156, 156, 192, 198, 198, 198, 28, 27, 11, 1, 11, 1, 1, 1, 1, 1, 1, 28, 82, 82, 82, 192, 192, 198, 197, 198, 198, 198, 198, 198, 198, 198, 28, 27, 28, 1, 28, 28] 198
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: 648
number of broken/clashed sets: 97
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071390 none CN(C(=O)CC(C)(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [9, 1, 9, 36, 36, 69, 90, 90, 90, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 9, 9, 9, 69, 69, 90, 89, 90, 90, 90, 90, 90, 90, 90, 1, 1, 1, 28, 1, 1] 198
rigid atoms, others: [1, 35, 36, 37, 39, 40, 9, 10, 11, 12, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 400
number of broken/clashed sets: 97
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071390 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071390
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071390/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071390
Building REAL250005071391
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071391'
/scratch/stefan/7916153/working/building/REAL250005071391 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071391

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071391/0 /scratch/stefan/7916153/working/building/REAL250005071391 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 520)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/520
`/scratch/stefan/7916153/working/3D/520' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071391.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071391.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071391/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071391 none CCCCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 179, 160, 81, 41, 81, 13, 41, 13, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 179, 179, 160, 160, 41, 41, 41, 13, 12, 13, 1, 13, 13] 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: 811
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071391 none CCCCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [148, 109, 84, 26, 9, 26, 1, 9, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 1, 148, 149, 149, 148, 148, 111, 111, 84, 84, 9, 9, 9, 1, 1, 1, 13, 1, 1] 201
rigid atoms, others: [32, 33, 34, 36, 37, 6, 8, 9, 10, 11, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 688
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071391 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071391
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071391/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071391
Building REAL250005071392
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071392'
/scratch/stefan/7916153/working/building/REAL250005071392 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071392

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071392/0 /scratch/stefan/7916153/working/building/REAL250005071392 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 521)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/521
`/scratch/stefan/7916153/working/3D/521' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071392.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071392.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071392/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071392 none CC(C)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 92, 93, 66, 92, 24, 66, 24, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 93, 93, 93, 93, 93, 93, 93, 66, 66, 66, 24, 23, 24, 1, 24, 24] 93
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: 255
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071392 none CC(C)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 27, 39, 9, 27, 1, 9, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 39, 39, 39, 39, 39, 39, 39, 9, 9, 9, 1, 1, 1, 24, 1, 1] 93
rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 164
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071392 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071392
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071392/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071392
Building REAL250005071393
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071393'
/scratch/stefan/7916153/working/building/REAL250005071393 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071393

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071393/0 /scratch/stefan/7916153/working/building/REAL250005071393 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 522)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/522
`/scratch/stefan/7916153/working/3D/522' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071393.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071393.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071393/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071393 none CCC(C)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [156, 141, 118, 141, 71, 118, 19, 71, 19, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 156, 156, 156, 156, 156, 141, 141, 141, 141, 71, 71, 71, 19, 18, 18, 1, 19, 19] 156
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: 546
number of broken/clashed sets: 73
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071393 none CCC(C)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [78, 58, 31, 58, 9, 31, 1, 9, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 84, 84, 84, 84, 84, 58, 58, 58, 58, 9, 9, 9, 1, 1, 1, 18, 1, 1] 156
rigid atoms, others: [32, 33, 34, 36, 37, 6, 8, 9, 10, 11, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 418
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071393 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071393
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071393/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071393
Building REAL250005071394
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071394'
/scratch/stefan/7916153/working/building/REAL250005071394 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071394

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071394/0 /scratch/stefan/7916153/working/building/REAL250005071394 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 523)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/523
`/scratch/stefan/7916153/working/3D/523' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071394.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071394.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071394/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071394 none CCC(CC)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [132, 126, 94, 126, 128, 56, 94, 20, 56, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 134, 134, 134, 134, 134, 126, 131, 131, 131, 131, 131, 56, 56, 56, 20, 19, 19, 1, 19, 19] 134
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: 521
number of broken/clashed sets: 72
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071394 none CCC(CC)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
134  conformations in input
total number of sets (complete confs): 134
using faster count positions algorithm for large data
unique positions, atoms: [62, 53, 27, 53, 62, 9, 27, 1, 9, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 71, 71, 71, 71, 71, 53, 67, 67, 67, 67, 67, 9, 9, 9, 1, 1, 1, 19, 1, 1] 134
rigid atoms, others: [35, 36, 37, 7, 40, 9, 10, 11, 12, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 501
number of broken/clashed sets: 72
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071394 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071394
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071394/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071394
Building REAL250005071395
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071395'
/scratch/stefan/7916153/working/building/REAL250005071395 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071395

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071395/0 /scratch/stefan/7916153/working/building/REAL250005071395 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 524)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/524
`/scratch/stefan/7916153/working/3D/524' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=NNC=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071395.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071395.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071395/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071395 none CN(C(=O)C1=NNC=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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: [7, 1, 7, 24, 24, 55, 55, 55, 55, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 7, 7, 7, 55, 55, 55, 1, 1, 1, 22, 1, 1] 96
rigid atoms, others: [32, 1, 9, 10, 11, 12, 20, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 136
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071395 none CN(C(=O)C1=NNC=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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: [32, 10, 1, 10, 1, 1, 1, 1, 1, 32, 55, 55, 55, 84, 84, 96, 96, 96, 96, 96, 55, 32, 32, 32, 1, 1, 1, 55, 55, 55, 96, 55, 55] 96
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32])
total number of confs: 279
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071395 none CN(C(=O)C1=NNC=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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: [51, 23, 51, 76, 76, 96, 96, 96, 96, 23, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 51, 51, 51, 96, 96, 96, 23, 22, 22, 1, 22, 22] 96
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: 253
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071395 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071395/1 /scratch/stefan/7916153/working/building/REAL250005071395 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 525)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/525
`/scratch/stefan/7916153/working/3D/525' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC=NN1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071395.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071395.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071395/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071395 none CN(C(=O)C1=CC=NN1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 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]
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, 25, 25, 72, 72, 72, 72, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 7, 7, 7, 72, 72, 72, 1, 1, 1, 27, 1, 1] 119
rigid atoms, others: [32, 1, 9, 10, 11, 12, 20, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 170
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071395 none CN(C(=O)C1=CC=NN1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 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]
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: [35, 11, 1, 11, 1, 1, 1, 1, 1, 35, 72, 72, 72, 111, 111, 119, 119, 119, 119, 119, 72, 35, 35, 35, 1, 1, 1, 72, 72, 72, 119, 72, 72] 119
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32])
total number of confs: 365
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071395 none CN(C(=O)C1=CC=NN1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 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]
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: [53, 27, 53, 95, 95, 119, 119, 119, 119, 27, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 53, 53, 53, 119, 119, 119, 27, 26, 26, 1, 27, 27] 119
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: 305
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071395 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071395
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071395/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071395/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071395
Building REAL250005071396
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071396'
/scratch/stefan/7916153/working/building/REAL250005071396 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071396

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071396/0 /scratch/stefan/7916153/working/building/REAL250005071396 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 526)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/526
`/scratch/stefan/7916153/working/3D/526' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071396.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071396.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071396/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071396 none CSC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 116, 101, 116, 69, 101, 23, 69, 23, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 144, 144, 144, 116, 116, 116, 116, 69, 69, 69, 23, 22, 23, 1, 23, 23] 144
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: 400
number of broken/clashed sets: 74
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071396 none CSC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [104, 47, 28, 47, 9, 28, 1, 9, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 104, 104, 104, 47, 47, 47, 47, 9, 9, 9, 1, 1, 1, 23, 1, 1] 144
rigid atoms, others: [32, 34, 35, 6, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 285
number of broken/clashed sets: 74
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071396 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071396
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071396/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071396
Building REAL250005071397
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071397'
/scratch/stefan/7916153/working/building/REAL250005071397 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071397

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071397/0 /scratch/stefan/7916153/working/building/REAL250005071397 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 527)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/527
`/scratch/stefan/7916153/working/3D/527' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071397.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071397.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071397/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071397 none CCOC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 90, 61, 90, 38, 61, 11, 38, 11, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 104, 104, 104, 104, 104, 90, 90, 90, 90, 38, 38, 38, 11, 10, 11, 1, 11, 11] 104
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: 350
number of broken/clashed sets: 53
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071397 none CCOC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [65, 65, 43, 21, 43, 9, 21, 1, 9, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 1, 65, 65, 65, 65, 65, 43, 43, 43, 43, 9, 9, 9, 1, 1, 1, 11, 1, 1] 104
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 219
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071397 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071397
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071397/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071397
Building REAL250005071398
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071398'
/scratch/stefan/7916153/working/building/REAL250005071398 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071398

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071398/0 /scratch/stefan/7916153/working/building/REAL250005071398 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 528)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/528
`/scratch/stefan/7916153/working/3D/528' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CNN=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071398.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071398.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071398/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071398 none CN(C(=O)C1=CNN=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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: [9, 1, 9, 28, 28, 49, 49, 49, 49, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 9, 9, 9, 49, 49, 49, 1, 1, 1, 22, 1, 1] 102
rigid atoms, others: [32, 1, 9, 10, 11, 12, 20, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 138
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071398 none CN(C(=O)C1=CNN=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [27, 9, 1, 9, 1, 1, 1, 1, 1, 27, 47, 47, 47, 79, 79, 91, 91, 91, 91, 91, 47, 27, 27, 27, 1, 1, 1, 47, 47, 47, 91, 47, 47] 91
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32])
total number of confs: 265
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071398 none CN(C(=O)C1=CNN=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 8, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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: [69, 22, 69, 101, 101, 102, 102, 102, 102, 22, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 69, 69, 69, 102, 102, 102, 22, 21, 21, 1, 22, 22] 102
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: 277
number of broken/clashed sets: 43
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071398 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071398
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071398/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071398
Building REAL250005071399
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071399'
/scratch/stefan/7916153/working/building/REAL250005071399 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071399

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071399/0 /scratch/stefan/7916153/working/building/REAL250005071399 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 529)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/529
`/scratch/stefan/7916153/working/3D/529' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071399.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071399.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071399/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071399 none COCCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 111, 111, 48, 28, 48, 8, 28, 8, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 201, 201, 201, 187, 184, 134, 134, 111, 111, 28, 28, 28, 8, 7, 8, 1, 8, 8] 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: 948
number of broken/clashed sets: 76
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071399 none COCCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 69, 70, 23, 9, 23, 1, 9, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 1, 167, 167, 167, 137, 135, 88, 88, 70, 70, 9, 9, 9, 1, 1, 1, 8, 1, 1] 201
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 766
number of broken/clashed sets: 76
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071399 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071399
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071399/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071399
Building REAL250005071400
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071400'
/scratch/stefan/7916153/working/building/REAL250005071400 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071400

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071400/0 /scratch/stefan/7916153/working/building/REAL250005071400 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 530)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/530
`/scratch/stefan/7916153/working/3D/530' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=NOC=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071400.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071400.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071400/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071400 none CN(C(=O)C1=NOC=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 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
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 32, 32, 93, 93, 93, 93, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 9, 9, 9, 93, 93, 1, 1, 1, 30, 1, 1] 180
rigid atoms, others: [1, 9, 10, 11, 12, 20, 26, 27, 28, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29])
total number of confs: 206
number of broken/clashed sets: 76
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071400 none CN(C(=O)C1=NOC=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 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
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [37, 10, 1, 10, 1, 1, 1, 1, 1, 37, 93, 93, 93, 160, 160, 180, 180, 180, 180, 180, 93, 37, 37, 37, 1, 1, 93, 93, 93, 180, 93, 93] 180
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 520
number of broken/clashed sets: 76
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071400 none CN(C(=O)C1=NOC=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 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
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [98, 30, 98, 149, 149, 180, 180, 180, 180, 30, 29, 11, 1, 11, 1, 1, 1, 1, 1, 1, 30, 98, 98, 98, 180, 180, 30, 29, 29, 1, 30, 30] 180
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 450
number of broken/clashed sets: 76
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071400 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071400
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071400/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071400
Building REAL250005071401
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071401'
/scratch/stefan/7916153/working/building/REAL250005071401 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071401

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071401/0 /scratch/stefan/7916153/working/building/REAL250005071401 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 531)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/531
`/scratch/stefan/7916153/working/3D/531' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=C(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071401.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071401.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071401/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071401 none CCC=C(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 191, 191, 111, 191, 58, 111, 16, 58, 16, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 201, 201, 201, 201, 201, 191, 191, 191, 191, 58, 58, 58, 16, 15, 16, 1, 16, 15] 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: 613
number of broken/clashed sets: 75
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071401 none CCC=C(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 89, 89, 32, 89, 9, 32, 1, 9, 1, 1, 1, 1, 6, 6, 15, 15, 16, 15, 15, 1, 150, 150, 150, 150, 150, 89, 89, 89, 89, 9, 9, 9, 1, 1, 1, 15, 1, 1] 201
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 573
number of broken/clashed sets: 75
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071401 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071401
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071401/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071401
Building REAL250005071402
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071402'
/scratch/stefan/7916153/working/building/REAL250005071402 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071402

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071402/0 /scratch/stefan/7916153/working/building/REAL250005071402 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 532)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/532
`/scratch/stefan/7916153/working/3D/532' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071402.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071402.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071402/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071402 none COC(C)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 119, 92, 119, 60, 92, 20, 60, 20, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 121, 121, 121, 119, 119, 119, 119, 60, 60, 60, 20, 19, 19, 1, 20, 20] 121
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: 393
number of broken/clashed sets: 53
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071402 none COC(C)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [75, 55, 24, 55, 9, 24, 1, 9, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 75, 75, 75, 55, 55, 55, 55, 9, 9, 9, 1, 1, 1, 20, 1, 1] 121
rigid atoms, others: [32, 34, 35, 6, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 278
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071402 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071402
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071402/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071402
Building REAL250005071403
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071403'
/scratch/stefan/7916153/working/building/REAL250005071403 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071403

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071403/0 /scratch/stefan/7916153/working/building/REAL250005071403 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 533)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/533
`/scratch/stefan/7916153/working/3D/533' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071403.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071403.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071403/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071403 none CC(C)OCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 177, 201, 124, 71, 45, 71, 12, 45, 12, 11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 201, 201, 124, 124, 45, 45, 45, 12, 11, 12, 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: 690
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071403 none CC(C)OCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 122, 146, 55, 19, 9, 19, 1, 9, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 1, 146, 146, 146, 146, 146, 146, 146, 55, 55, 9, 9, 9, 1, 1, 1, 12, 1, 1] 201
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 471
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071403 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071403
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071403/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071403
Building REAL250005071404
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071404'
/scratch/stefan/7916153/working/building/REAL250005071404 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071404

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071404/0 /scratch/stefan/7916153/working/building/REAL250005071404 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 534)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/534
`/scratch/stefan/7916153/working/3D/534' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCOCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071404.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071404.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071404/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071404 none CCCOCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 145, 99, 57, 44, 57, 14, 44, 14, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 184, 184, 99, 99, 44, 44, 44, 14, 13, 14, 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: 730
number of broken/clashed sets: 73
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071404 none CCCOCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 102, 62, 29, 11, 8, 11, 1, 8, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 1, 140, 140, 140, 140, 140, 102, 102, 29, 29, 8, 8, 8, 1, 1, 1, 14, 1, 1] 201
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 589
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071404 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071404
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071404/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071404
Building REAL250005071405
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071405'
/scratch/stefan/7916153/working/building/REAL250005071405 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071405

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071405/0 /scratch/stefan/7916153/working/building/REAL250005071405 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 535)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/535
`/scratch/stefan/7916153/working/3D/535' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1CCOC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071405.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071405.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071405/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071405 none CN(C(=O)C1CCOC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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: [8, 1, 8, 20, 20, 37, 37, 37, 37, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 8, 8, 8, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 18, 1, 1] 77
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 131
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071405 none CN(C(=O)C1CCOC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [19, 6, 1, 6, 1, 1, 1, 1, 1, 19, 37, 37, 37, 61, 61, 77, 77, 77, 77, 77, 37, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 77, 37, 37] 77
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36])
total number of confs: 230
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071405 none CN(C(=O)C1CCOC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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: [41, 18, 41, 59, 59, 77, 77, 77, 77, 18, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 41, 41, 41, 77, 77, 77, 77, 77, 77, 77, 18, 18, 18, 1, 18, 18] 77
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: 229
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071405 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071405
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071405/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071405
Building REAL250005071406
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071406'
/scratch/stefan/7916153/working/building/REAL250005071406 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071406

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071406/0 /scratch/stefan/7916153/working/building/REAL250005071406 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 536)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/536
`/scratch/stefan/7916153/working/3D/536' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(OC)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071406.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071406.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071406/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071406 none CCC(OC)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [188, 183, 111, 183, 197, 57, 111, 16, 57, 16, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 196, 196, 196, 196, 196, 183, 197, 197, 197, 57, 57, 57, 16, 15, 16, 1, 16, 16] 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: 822
number of broken/clashed sets: 94
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071406 none CCC(OC)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [105, 79, 29, 79, 109, 9, 29, 1, 9, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 117, 117, 117, 117, 117, 79, 109, 109, 109, 9, 9, 9, 1, 1, 1, 16, 1, 1] 201
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 661
number of broken/clashed sets: 94
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071406 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071406
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071406/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071406
Building REAL250005071407
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071407'
/scratch/stefan/7916153/working/building/REAL250005071407 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071407

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071407/0 /scratch/stefan/7916153/working/building/REAL250005071407 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 537)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/537
`/scratch/stefan/7916153/working/3D/537' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071407.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071407.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071407/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071407 none COC(C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 180, 200, 99, 57, 99, 15, 57, 15, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 201, 201, 201, 200, 200, 200, 200, 180, 180, 57, 57, 57, 15, 14, 15, 1, 15, 15] 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: 767
number of broken/clashed sets: 98
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071407 none COC(C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 123, 87, 121, 26, 9, 26, 1, 9, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 136, 136, 136, 123, 123, 123, 123, 87, 87, 9, 9, 9, 1, 1, 1, 15, 1, 1] 201
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 572
number of broken/clashed sets: 98
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071407 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071407
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071407/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071407
Building REAL250005071408
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071408'
/scratch/stefan/7916153/working/building/REAL250005071408 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071408

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071408/0 /scratch/stefan/7916153/working/building/REAL250005071408 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 538)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/538
`/scratch/stefan/7916153/working/3D/538' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071408.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071408.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071408/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071408 none C=CCCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 183, 92, 51, 92, 15, 51, 15, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 201, 201, 201, 201, 201, 183, 183, 51, 51, 51, 15, 14, 15, 1, 15, 15] 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: 757
number of broken/clashed sets: 76
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071408 none C=CCCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 113, 89, 24, 9, 24, 1, 9, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 154, 154, 154, 113, 113, 89, 89, 9, 9, 9, 1, 1, 1, 15, 1, 1] 201
rigid atoms, others: [32, 34, 35, 6, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 618
number of broken/clashed sets: 76
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071408 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071408
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071408/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071408
Building REAL250005071409
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071409'
/scratch/stefan/7916153/working/building/REAL250005071409 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071409

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071409/0 /scratch/stefan/7916153/working/building/REAL250005071409 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 539)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/539
`/scratch/stefan/7916153/working/3D/539' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071409.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071409.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071409/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071409 none CCOCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 167, 153, 77, 42, 77, 15, 42, 15, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 201, 201, 201, 201, 201, 167, 167, 153, 153, 42, 42, 42, 15, 14, 15, 1, 15, 15] 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: 688
number of broken/clashed sets: 74
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071409 none CCOCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [153, 147, 93, 81, 24, 9, 24, 1, 9, 1, 1, 1, 1, 5, 5, 14, 14, 14, 14, 14, 1, 153, 153, 153, 153, 153, 93, 93, 81, 81, 9, 9, 9, 1, 1, 1, 15, 1, 1] 201
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 497
number of broken/clashed sets: 74
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071409 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071409
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071409/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071409
Building REAL250005071410
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071410'
/scratch/stefan/7916153/working/building/REAL250005071410 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071410

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071410/0 /scratch/stefan/7916153/working/building/REAL250005071410 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 540)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/540
`/scratch/stefan/7916153/working/3D/540' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071410.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071410.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071410/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071410 none COCC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 170, 120, 170, 79, 120, 22, 79, 22, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 22, 201, 201, 201, 201, 201, 170, 170, 170, 170, 79, 79, 79, 22, 21, 21, 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: 762
number of broken/clashed sets: 107
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071410 none COCC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 107, 48, 23, 48, 9, 23, 1, 9, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 144, 144, 144, 107, 107, 48, 48, 48, 48, 9, 9, 9, 1, 1, 1, 21, 1, 1] 201
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 556
number of broken/clashed sets: 107
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071410 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071410
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071410/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071410
Building REAL250005071411
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071411'
/scratch/stefan/7916153/working/building/REAL250005071411 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071411

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071411/0 /scratch/stefan/7916153/working/building/REAL250005071411 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 541)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/541
`/scratch/stefan/7916153/working/3D/541' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCOCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071411.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071411.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071411/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071411 none C=CCOCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 116, 87, 39, 27, 39, 10, 27, 10, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 201, 201, 201, 201, 201, 87, 87, 27, 27, 27, 10, 9, 10, 1, 10, 10] 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: 799
number of broken/clashed sets: 58
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071411 none C=CCOCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 137, 61, 36, 10, 7, 10, 1, 7, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 1, 168, 168, 168, 137, 137, 36, 36, 7, 7, 7, 1, 1, 1, 10, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 7, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 667
number of broken/clashed sets: 58
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071411 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071411
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071411/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071411
Building REAL250005071412
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071412'
/scratch/stefan/7916153/working/building/REAL250005071412 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071412

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071412/0 /scratch/stefan/7916153/working/building/REAL250005071412 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 542)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/542
`/scratch/stefan/7916153/working/3D/542' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=COC=N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071412.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071412.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071412/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071412 none CN(C(=O)C1=COC=N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 1, 12, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 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
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 21, 21, 37, 37, 37, 37, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 7, 7, 7, 37, 37, 1, 1, 1, 20, 1, 1] 60
rigid atoms, others: [1, 9, 10, 11, 12, 20, 26, 27, 28, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29])
total number of confs: 109
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071412 none CN(C(=O)C1=COC=N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 1, 12, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 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
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [22, 8, 1, 8, 1, 1, 1, 1, 1, 22, 37, 37, 37, 53, 53, 60, 60, 60, 60, 60, 37, 22, 22, 22, 1, 1, 37, 37, 37, 60, 37, 37] 60
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 180
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071412 none CN(C(=O)C1=COC=N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 1, 12, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 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
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [34, 20, 34, 52, 52, 60, 60, 60, 60, 20, 20, 10, 1, 10, 1, 1, 1, 1, 1, 1, 20, 34, 34, 34, 60, 60, 20, 20, 20, 1, 20, 20] 60
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 147
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071412 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071412
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071412/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071412
Building REAL250005071413
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071413'
/scratch/stefan/7916153/working/building/REAL250005071413 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071413

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071413/0 /scratch/stefan/7916153/working/building/REAL250005071413 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 543)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/543
`/scratch/stefan/7916153/working/3D/543' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C#N)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071413.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071413.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071413/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071413 none CC(C#N)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 81, 98, 98, 61, 81, 26, 61, 26, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 98, 98, 98, 98, 61, 61, 61, 26, 25, 26, 1, 26, 26] 98
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: 319
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071413 none CC(C#N)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [48, 25, 48, 48, 9, 25, 1, 9, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 48, 48, 48, 48, 9, 9, 9, 1, 1, 1, 26, 1, 1] 98
rigid atoms, others: [32, 6, 8, 9, 10, 11, 19, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 213
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071413 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071413
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071413/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071413
Building REAL250005071414
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071414'
/scratch/stefan/7916153/working/building/REAL250005071414 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071414

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071414/0 /scratch/stefan/7916153/working/building/REAL250005071414 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 544)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/544
`/scratch/stefan/7916153/working/3D/544' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071414.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071414.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071414/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071414 none CCCC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 193, 166, 120, 166, 68, 120, 23, 68, 23, 22, 7, 1, 7, 1, 1, 1, 1, 1, 1, 23, 201, 201, 201, 201, 196, 198, 198, 166, 166, 166, 166, 68, 68, 68, 23, 22, 23, 1, 23, 23] 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: 797
number of broken/clashed sets: 93
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071414 none CCCC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 113, 69, 30, 69, 9, 30, 1, 9, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 129, 129, 129, 129, 124, 119, 119, 69, 69, 69, 69, 9, 9, 9, 1, 1, 1, 23, 1, 1] 201
rigid atoms, others: [35, 36, 37, 7, 40, 9, 10, 11, 12, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 615
number of broken/clashed sets: 93
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071414 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071414
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071414/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071414
Building REAL250005071415
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071415'
/scratch/stefan/7916153/working/building/REAL250005071415 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071415

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071415/0 /scratch/stefan/7916153/working/building/REAL250005071415 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 545)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/545
`/scratch/stefan/7916153/working/3D/545' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CCC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071415.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071415.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071415/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071415 none CN(C(=O)CCC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 20, 20, 67, 82, 126, 126, 1, 1, 1, 1, 7, 7, 15, 16, 16, 16, 16, 1, 7, 7, 7, 67, 67, 92, 92, 126, 126, 126, 126, 126, 1, 1, 1, 16, 1, 1] 201
rigid atoms, others: [1, 34, 35, 37, 38, 33, 9, 10, 11, 12, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 580
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071415 none CN(C(=O)CCC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [87, 31, 7, 31, 3, 1, 1, 1, 1, 87, 126, 126, 126, 195, 195, 201, 201, 201, 201, 201, 126, 87, 87, 87, 7, 7, 3, 3, 1, 1, 1, 1, 1, 126, 126, 126, 201, 126, 126] 201
rigid atoms, others: [32, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38])
total number of confs: 654
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071415 none CN(C(=O)CCC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 16, 42, 81, 81, 153, 170, 201, 201, 16, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 42, 42, 42, 153, 153, 172, 172, 201, 201, 201, 201, 201, 16, 16, 16, 1, 16, 16] 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: 761
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071415 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071415
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071415/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071415
Building REAL250005071416
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071416'
/scratch/stefan/7916153/working/building/REAL250005071416 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071416

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071416/0 /scratch/stefan/7916153/working/building/REAL250005071416 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 546)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/546
`/scratch/stefan/7916153/working/3D/546' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1CC=CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071416.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071416.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071416/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071416 none CN(C(=O)C1CC=CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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, 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, 20, 20, 40, 40, 40, 40, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 23, 1, 1] 98
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 148
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071416 none CN(C(=O)C1CC=CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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, 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: [22, 6, 1, 6, 1, 1, 1, 1, 1, 22, 40, 40, 40, 73, 73, 98, 98, 98, 98, 98, 40, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 98, 40, 40] 98
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36])
total number of confs: 278
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071416 none CN(C(=O)C1CC=CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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, 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: [50, 24, 50, 77, 77, 98, 98, 98, 98, 24, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 98, 98, 98, 98, 98, 98, 98, 24, 23, 23, 1, 24, 24] 98
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: 299
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071416 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071416
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071416/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071416
Building REAL250005071417
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071417'
/scratch/stefan/7916153/working/building/REAL250005071417 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071417

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071417/0 /scratch/stefan/7916153/working/building/REAL250005071417 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 547)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/547
`/scratch/stefan/7916153/working/3D/547' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CC1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071417.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071417.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071417/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071417 none CN(C(=O)CC1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 21, 21, 67, 102, 102, 102, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 7, 7, 7, 67, 67, 102, 102, 102, 102, 102, 102, 102, 1, 1, 1, 21, 1, 1] 144
rigid atoms, others: [1, 34, 35, 37, 38, 33, 9, 10, 11, 12, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 397
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071417 none CN(C(=O)CC1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [70, 28, 6, 28, 1, 1, 1, 1, 1, 70, 102, 102, 102, 140, 140, 144, 144, 144, 144, 144, 102, 70, 70, 70, 6, 6, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 144, 102, 102] 144
rigid atoms, others: [32, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38])
total number of confs: 463
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071417 none CN(C(=O)CC1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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, 21, 47, 75, 75, 124, 144, 144, 144, 21, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 21, 47, 47, 47, 124, 124, 144, 144, 144, 144, 144, 144, 144, 21, 20, 21, 1, 21, 21] 144
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: 525
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071417 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071417
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071417/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071417
Building REAL250005071418
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071418'
/scratch/stefan/7916153/working/building/REAL250005071418 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071418

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071418/0 /scratch/stefan/7916153/working/building/REAL250005071418 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 548)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/548
`/scratch/stefan/7916153/working/3D/548' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)C1CC1)

`REAL250005071418.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071418.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071418/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071418 none CC(C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)C1CC1 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', 'C.3', 'C.3', 'H', '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, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [94, 88, 61, 88, 21, 61, 21, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 94, 96, 96, 94, 94, 94, 94, 61, 61, 61, 21, 20, 21, 1, 21, 21, 96, 96, 96, 96, 96] 96
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, 36, 37, 38])
total number of confs: 276
number of broken/clashed sets: 47
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071418 none CC(C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)C1CC1 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', 'C.3', 'C.3', 'H', '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, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [45, 28, 9, 28, 1, 9, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 45, 54, 54, 45, 45, 45, 45, 9, 9, 9, 1, 1, 1, 21, 1, 1, 54, 54, 54, 54, 54] 96
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 17, 28, 29, 30] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 34, 35, 36, 37, 38])
total number of confs: 222
number of broken/clashed sets: 47
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071418 none CC(C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)C1CC1 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', 'C.3', 'C.3', 'H', '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, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 12, 12, 25, 25, 54, 54, 54, 90, 90, 96, 96, 96, 96, 96, 54, 1, 1, 1, 6, 6, 6, 6, 25, 25, 25, 54, 54, 54, 96, 54, 54, 1, 1, 1, 1, 1] 96
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: 290
number of broken/clashed sets: 47
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071418 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071418
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071418/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071418
Building REAL250005071419
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071419'
/scratch/stefan/7916153/working/building/REAL250005071419 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071419

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071419/0 /scratch/stefan/7916153/working/building/REAL250005071419 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 549)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/549
`/scratch/stefan/7916153/working/3D/549' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071419.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071419.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071419/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071419 none CC=C(C)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 99, 136, 74, 99, 27, 74, 27, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 27, 136, 136, 136, 136, 136, 136, 136, 74, 74, 74, 27, 26, 26, 1, 27, 27] 136
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: 418
number of broken/clashed sets: 65
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071419 none CC=C(C)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [62, 62, 28, 62, 9, 28, 1, 9, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 62, 62, 62, 62, 62, 62, 62, 9, 9, 9, 1, 1, 1, 26, 1, 1] 136
rigid atoms, others: [32, 34, 35, 6, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 218
number of broken/clashed sets: 65
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071419 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071419
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071419/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071419
Building REAL250005071420
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071420'
/scratch/stefan/7916153/working/building/REAL250005071420 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071420

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071420/0 /scratch/stefan/7916153/working/building/REAL250005071420 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 550)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/550
`/scratch/stefan/7916153/working/3D/550' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)C1)

`REAL250005071420.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071420.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071420/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071420 none CC1CC(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [44, 44, 44, 22, 8, 22, 1, 8, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 44, 44, 44, 44, 44, 44, 44, 44, 8, 8, 8, 1, 1, 1, 19, 1, 1, 44, 44] 85
rigid atoms, others: [32, 33, 35, 36, 6, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 37, 38])
total number of confs: 156
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071420 none CC1CC(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 22, 22, 44, 44, 44, 75, 75, 85, 85, 85, 85, 85, 44, 1, 2, 2, 2, 1, 1, 1, 1, 22, 22, 22, 44, 44, 44, 85, 44, 44, 1, 1] 85
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: 265
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071420 none CC1CC(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [85, 85, 85, 67, 45, 67, 19, 45, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 85, 85, 85, 85, 85, 85, 85, 85, 45, 45, 45, 19, 19, 19, 1, 19, 19, 85, 85] 85
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: 248
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071420 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071420
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071420/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071420
Building REAL250005071421
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071421'
/scratch/stefan/7916153/working/building/REAL250005071421 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071421

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071421/0 /scratch/stefan/7916153/working/building/REAL250005071421 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 551)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/551
`/scratch/stefan/7916153/working/3D/551' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C=C1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071421.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071421.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071421/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071421 none CN(C(=O)C=C1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 18, 18, 61, 61, 61, 61, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 7, 7, 7, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 23, 1, 1] 127
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 192
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071421 none CN(C(=O)C=C1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [36, 9, 1, 9, 1, 1, 1, 1, 1, 36, 61, 61, 61, 103, 103, 127, 127, 127, 127, 127, 61, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 127, 61, 61] 127
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36])
total number of confs: 379
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071421 none CN(C(=O)C=C1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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, 7, 7]
0  hydrogens need rotated
127  conformations in input
total number of sets (complete confs): 127
using faster count positions algorithm for large data
unique positions, atoms: [47, 23, 47, 80, 80, 127, 127, 127, 127, 23, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 47, 47, 47, 127, 127, 127, 127, 127, 127, 127, 23, 22, 23, 1, 23, 23] 127
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: 375
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071421 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071421
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071421/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071421
Building REAL250005071422
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071422'
/scratch/stefan/7916153/working/building/REAL250005071422 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071422

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071422/0 /scratch/stefan/7916153/working/building/REAL250005071422 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 552)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/552
`/scratch/stefan/7916153/working/3D/552' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=C(F)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071422.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071422.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071422/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071422 none CC(C)=C(F)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 5, 1, 15, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 112, 146, 79, 112, 26, 79, 26, 25, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 146, 146, 146, 146, 146, 146, 79, 79, 79, 26, 25, 25, 1, 26, 26] 146
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: 441
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071422 none CC(C)=C(F)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 5, 1, 15, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [58, 58, 58, 30, 58, 9, 30, 1, 9, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 58, 58, 58, 58, 58, 58, 9, 9, 9, 1, 1, 1, 26, 1, 1] 146
rigid atoms, others: [32, 34, 35, 7, 9, 10, 11, 12, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 198
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071422 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071422
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071422/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071422
Building REAL250005071423
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071423'
/scratch/stefan/7916153/working/building/REAL250005071423 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071423

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071423/0 /scratch/stefan/7916153/working/building/REAL250005071423 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 553)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/553
`/scratch/stefan/7916153/working/3D/553' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CCCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071423.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071423.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071423/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071423 none CN(C(=O)C1=CCCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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, 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, 1, 7, 22, 22, 40, 40, 40, 40, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 8, 8, 8, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 27, 1, 1] 73
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 129
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071423 none CN(C(=O)C1=CCCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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, 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: [21, 8, 1, 8, 1, 1, 1, 1, 1, 21, 40, 40, 40, 59, 59, 73, 73, 73, 73, 73, 40, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 73, 40, 40] 73
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36])
total number of confs: 201
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071423 none CN(C(=O)C1=CCCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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, 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: [53, 27, 53, 73, 73, 73, 73, 73, 73, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 53, 53, 53, 73, 73, 73, 73, 73, 73, 73, 27, 27, 27, 1, 26, 26] 73
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: 193
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071423 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071423
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071423/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071423
Building REAL250005071424
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071424'
/scratch/stefan/7916153/working/building/REAL250005071424 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071424

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071424/0 /scratch/stefan/7916153/working/building/REAL250005071424 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 554)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/554
`/scratch/stefan/7916153/working/3D/554' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1CC1(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071424.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071424.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071424/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071424 none CN(C(=O)C1CC1(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [9, 1, 9, 25, 25, 48, 48, 48, 48, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 9, 9, 9, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 23, 1, 1] 93
rigid atoms, others: [1, 34, 35, 37, 38, 33, 9, 10, 11, 12, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 175
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071424 none CN(C(=O)C1CC1(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [19, 6, 1, 6, 1, 1, 1, 1, 1, 19, 48, 48, 48, 82, 82, 93, 93, 93, 93, 93, 48, 19, 19, 19, 1, 1, 1, 2, 2, 2, 2, 2, 2, 48, 48, 48, 93, 48, 48] 93
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 274
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071424 none CN(C(=O)C1CC1(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [56, 23, 56, 79, 79, 93, 93, 93, 93, 23, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 56, 56, 56, 93, 93, 93, 93, 93, 93, 93, 93, 93, 23, 22, 23, 1, 23, 23] 93
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: 262
number of broken/clashed sets: 38
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071424 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071424
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071424/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071424
Building REAL250005071425
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071425'
/scratch/stefan/7916153/working/building/REAL250005071425 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071425

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071425/0 /scratch/stefan/7916153/working/building/REAL250005071425 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 555)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/555
`/scratch/stefan/7916153/working/3D/555' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)[C@H]1CC1(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071425.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071425.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071425/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071425 none CN(C(=O)[C@H]1CC1(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 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, 7]
dock color type numbers: [7, 7, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 21, 21, 43, 43, 43, 43, 43, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 8, 8, 8, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 22, 1, 1] 85
rigid atoms, others: [1, 34, 35, 37, 38, 33, 10, 11, 12, 13, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 155
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071425 none CN(C(=O)[C@H]1CC1(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 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, 7]
dock color type numbers: [7, 7, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 43, 43, 43, 76, 76, 85, 85, 85, 85, 85, 43, 20, 20, 20, 1, 1, 2, 2, 2, 2, 2, 2, 43, 43, 43, 85, 43, 43] 85
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 25, 26] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 257
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071425 none CN(C(=O)[C@H]1CC1(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 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, 7]
dock color type numbers: [7, 7, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [48, 22, 48, 70, 70, 85, 85, 85, 85, 85, 22, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 85, 85, 85, 85, 85, 85, 85, 85, 22, 22, 22, 1, 22, 22] 85
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: 242
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071425 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071425
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071425/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071425
Building REAL250005071426
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071426'
/scratch/stefan/7916153/working/building/REAL250005071426 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071426

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071426/0 /scratch/stefan/7916153/working/building/REAL250005071426 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 556)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/556
`/scratch/stefan/7916153/working/3D/556' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)[C@@H]1CCCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071426.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071426.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071426/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071426 none CN(C(=O)[C@@H]1CCCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', '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, 7, 5, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 23, 23, 46, 46, 46, 46, 46, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 9, 9, 9, 46, 46, 46, 46, 46, 46, 1, 1, 1, 18, 1, 1] 81
rigid atoms, others: [32, 1, 35, 36, 33, 10, 11, 12, 13, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 152
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071426 none CN(C(=O)[C@@H]1CCCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', '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, 7, 5, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 46, 46, 46, 72, 72, 81, 81, 81, 81, 81, 46, 25, 25, 25, 1, 1, 1, 1, 1, 1, 46, 46, 46, 81, 46, 46] 81
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36])
total number of confs: 249
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071426 none CN(C(=O)[C@@H]1CCCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', '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, 7, 5, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [48, 18, 48, 69, 69, 81, 81, 81, 81, 81, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 48, 48, 48, 81, 81, 81, 81, 81, 81, 18, 18, 18, 1, 18, 18] 81
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: 235
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071426 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071426
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071426/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071426
Building REAL250005071427
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071427'
/scratch/stefan/7916153/working/building/REAL250005071427 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071427

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071427/0 /scratch/stefan/7916153/working/building/REAL250005071427 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 557)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/557
`/scratch/stefan/7916153/working/3D/557' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071427.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071427.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071427/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071427 none CCC(C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 189, 164, 189, 74, 40, 74, 11, 40, 11, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 201, 201, 201, 201, 201, 189, 189, 189, 189, 164, 164, 40, 40, 40, 11, 10, 11, 1, 11, 11] 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: 820
number of broken/clashed sets: 105
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071427 none CCC(C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 120, 82, 120, 23, 9, 23, 1, 9, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 1, 146, 146, 146, 146, 146, 120, 120, 120, 120, 82, 82, 9, 9, 9, 1, 1, 1, 11, 1, 1] 201
rigid atoms, others: [35, 36, 37, 7, 40, 9, 10, 11, 12, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 660
number of broken/clashed sets: 105
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071427 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071427
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071427/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071427
Building REAL250005071428
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071428'
/scratch/stefan/7916153/working/building/REAL250005071428 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071428

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071428/0 /scratch/stefan/7916153/working/building/REAL250005071428 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 558)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/558
`/scratch/stefan/7916153/working/3D/558' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071428.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071428.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071428/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071428 none C#CCCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 104, 95, 39, 23, 39, 8, 23, 8, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 201, 192, 190, 118, 118, 95, 95, 23, 23, 23, 8, 7, 8, 1, 8, 8] 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: 916
number of broken/clashed sets: 81
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071428 none C#CCCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 74, 65, 21, 9, 21, 1, 9, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 1, 158, 150, 149, 85, 85, 65, 65, 9, 9, 9, 1, 1, 1, 8, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 7, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 742
number of broken/clashed sets: 81
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071428 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071428
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071428/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071428
Building REAL250005071429
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071429'
/scratch/stefan/7916153/working/building/REAL250005071429 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071429

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071429/0 /scratch/stefan/7916153/working/building/REAL250005071429 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 559)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/559
`/scratch/stefan/7916153/working/3D/559' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CC(C)(C)O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071429.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071429.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071429/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071429 none CN(C(=O)CC(C)(C)O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 12, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 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, 7, 7, 7, 7]
1  hydrogens need rotated
336  conformations in input
total number of sets (complete confs): 336
using faster count positions algorithm for large data
unique positions, atoms: [46, 16, 46, 69, 69, 103, 112, 112, 112, 16, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 46, 46, 46, 103, 103, 112, 112, 112, 112, 112, 112, 336, 16, 15, 15, 1, 15, 15] 336
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: 739
number of broken/clashed sets: 163
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071429 none CN(C(=O)CC(C)(C)O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 12, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 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, 7, 7, 7, 7]
1  hydrogens need rotated
336  conformations in input
total number of sets (complete confs): 336
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 23, 23, 63, 76, 76, 75, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 9, 9, 9, 63, 63, 76, 76, 76, 76, 76, 76, 228, 1, 1, 1, 15, 1, 1] 336
rigid atoms, others: [1, 34, 35, 37, 38, 33, 9, 10, 11, 12, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 547
number of broken/clashed sets: 163
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071429 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071429
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071429/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071429
Building REAL250005071430
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071430'
/scratch/stefan/7916153/working/building/REAL250005071430 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071430

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071430/0 /scratch/stefan/7916153/working/building/REAL250005071430 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 560)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/560
`/scratch/stefan/7916153/working/3D/560' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[C@@H](O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071430.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071430.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071430/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071430 none CC(C)[C@@H](O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 7, 12, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
513  conformations in input
total number of sets (complete confs): 513
using faster count positions algorithm for large data
unique positions, atoms: [171, 157, 171, 109, 157, 157, 59, 109, 20, 59, 20, 19, 5, 1, 5, 1, 1, 1, 1, 1, 1, 20, 171, 171, 171, 171, 171, 171, 171, 471, 59, 59, 59, 20, 19, 20, 1, 20, 20] 513
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: 1098
number of broken/clashed sets: 257
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071430 none CC(C)[C@@H](O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 7, 12, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
513  conformations in input
total number of sets (complete confs): 513
using faster count positions algorithm for large data
unique positions, atoms: [107, 75, 107, 31, 75, 75, 9, 31, 1, 9, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 107, 107, 107, 107, 107, 107, 107, 225, 9, 9, 9, 1, 1, 1, 20, 1, 1] 513
rigid atoms, others: [33, 34, 35, 37, 38, 8, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 716
number of broken/clashed sets: 257
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071430 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071430
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071430/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071430
Building REAL250005071431
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071431'
/scratch/stefan/7916153/working/building/REAL250005071431 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071431

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071431/0 /scratch/stefan/7916153/working/building/REAL250005071431 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 561)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/561
`/scratch/stefan/7916153/working/3D/561' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071431.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071431.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071431/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071431 none CCC(C)=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 126, 126, 126, 93, 56, 93, 21, 56, 21, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 201, 201, 201, 201, 201, 126, 126, 126, 126, 56, 56, 56, 21, 20, 20, 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: 832
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071431 none CCC(C)=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 57, 57, 57, 28, 9, 28, 1, 9, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 99, 99, 99, 99, 99, 57, 57, 57, 57, 9, 9, 9, 1, 1, 1, 20, 1, 1] 201
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 448
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071431 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071431
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071431/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071431
Building REAL250005071432
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071432'
/scratch/stefan/7916153/working/building/REAL250005071432 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071432

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071432/0 /scratch/stefan/7916153/working/building/REAL250005071432 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 562)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/562
`/scratch/stefan/7916153/working/3D/562' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C#CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071432.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071432.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071432/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071432 none CC(C)C#CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 72, 53, 72, 22, 53, 22, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 72, 72, 72, 72, 72, 72, 72, 53, 53, 53, 22, 21, 22, 1, 22, 22] 72
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: 193
number of broken/clashed sets: 35
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071432 none CC(C)C#CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 29, 29, 29, 9, 29, 1, 9, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 29, 29, 29, 29, 29, 29, 29, 9, 9, 9, 1, 1, 1, 22, 1, 1] 72
rigid atoms, others: [32, 33, 35, 36, 7, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 104
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071432 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071432
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071432/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071432
Building REAL250005071433
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071433'
/scratch/stefan/7916153/working/building/REAL250005071433 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071433

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071433/0 /scratch/stefan/7916153/working/building/REAL250005071433 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 563)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/563
`/scratch/stefan/7916153/working/3D/563' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C#CC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071433.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071433.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071433/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071433 none CN(C(=O)C#CC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', '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']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 7, 7, 23, 24, 24, 24, 24, 1, 7, 7, 7, 21, 21, 21, 21, 21, 1, 1, 1, 24, 1, 1] 60
rigid atoms, others: [1, 34, 33, 9, 10, 11, 12, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 95
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071433 none CN(C(=O)C#CC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', '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']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 46, 46, 60, 60, 60, 60, 60, 21, 7, 7, 7, 1, 1, 1, 1, 1, 21, 21, 21, 60, 21, 21] 60
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34])
total number of confs: 156
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071433 none CN(C(=O)C#CC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', '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']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [43, 24, 43, 60, 60, 60, 60, 60, 60, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 43, 43, 43, 60, 60, 60, 60, 60, 24, 24, 24, 1, 24, 24] 60
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: 159
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071433 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071433
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071433/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071433
Building REAL250005071434
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071434'
/scratch/stefan/7916153/working/building/REAL250005071434 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071434

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071434/0 /scratch/stefan/7916153/working/building/REAL250005071434 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 564)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/564
`/scratch/stefan/7916153/working/3D/564' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071434.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071434.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071434/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071434 none CCC(=O)N(C)C1CN(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 106, 74, 106, 26, 74, 26, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 108, 108, 108, 108, 108, 74, 74, 74, 26, 25, 26, 1, 26, 26] 108
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: 301
number of broken/clashed sets: 39
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071434 none CCC(=O)N(C)C1CN(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [53, 25, 9, 25, 1, 9, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 53, 53, 53, 53, 53, 9, 9, 9, 1, 1, 1, 26, 1, 1] 108
rigid atoms, others: [4, 6, 7, 8, 9, 17, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 29])
total number of confs: 226
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071434 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071434
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071434/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071434
Building REAL250005071435
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071435'
/scratch/stefan/7916153/working/building/REAL250005071435 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071435

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071435/0 /scratch/stefan/7916153/working/building/REAL250005071435 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 565)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/565
`/scratch/stefan/7916153/working/3D/565' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071435.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071435.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071435/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071435 none COCCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 180, 101, 53, 101, 16, 53, 16, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 201, 201, 201, 200, 200, 180, 180, 53, 53, 53, 16, 15, 16, 1, 16, 16] 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: 80
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071435 none COCCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 117, 92, 25, 9, 25, 1, 9, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 155, 155, 155, 117, 117, 92, 92, 9, 9, 9, 1, 1, 1, 16, 1, 1] 201
rigid atoms, others: [32, 34, 35, 6, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 556
number of broken/clashed sets: 80
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071435 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071435
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071435/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071435
Building REAL250005071436
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071436'
/scratch/stefan/7916153/working/building/REAL250005071436 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071436

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071436/0 /scratch/stefan/7916153/working/building/REAL250005071436 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 566)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/566
`/scratch/stefan/7916153/working/3D/566' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071436.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071436.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071436/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071436 none CN(C(=O)C1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 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]
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]
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: [9, 1, 9, 25, 25, 53, 53, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 9, 9, 9, 53, 53, 53, 53, 53, 1, 1, 1, 25, 1, 1] 118
rigid atoms, others: [32, 1, 7, 8, 9, 10, 18, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 184
number of broken/clashed sets: 49
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071436 none CN(C(=O)C1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 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]
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]
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: [21, 7, 1, 7, 1, 1, 1, 21, 53, 53, 53, 105, 105, 118, 118, 118, 118, 118, 53, 21, 21, 21, 1, 1, 1, 1, 1, 53, 53, 53, 118, 53, 53] 118
rigid atoms, others: [2, 4, 5, 6, 22, 23, 24, 25, 26] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32])
total number of confs: 340
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071436 none CN(C(=O)C1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 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]
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]
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: [77, 25, 77, 98, 98, 118, 118, 25, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 77, 77, 77, 118, 118, 118, 118, 118, 25, 24, 25, 1, 25, 25] 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])
total number of confs: 340
number of broken/clashed sets: 49
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071436 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071436
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071436/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071436
Building REAL250005071437
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071437'
/scratch/stefan/7916153/working/building/REAL250005071437 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071437

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071437/0 /scratch/stefan/7916153/working/building/REAL250005071437 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 567)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/567
`/scratch/stefan/7916153/working/3D/567' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071437.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071437.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071437/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071437 none CN(C(=O)C1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 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]
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]
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, 22, 22, 43, 43, 43, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 16, 1, 8, 8, 8, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 16, 1, 1] 77
rigid atoms, others: [32, 1, 34, 35, 8, 9, 10, 11, 19, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 150
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071437 none CN(C(=O)C1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 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]
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]
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: [20, 6, 1, 6, 1, 1, 1, 1, 20, 43, 43, 43, 68, 68, 77, 77, 77, 77, 77, 43, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 77, 43, 43] 77
rigid atoms, others: [2, 4, 5, 6, 7, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35])
total number of confs: 233
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071437 none CN(C(=O)C1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 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]
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]
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: [43, 17, 43, 61, 61, 77, 77, 77, 17, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 43, 43, 43, 77, 77, 77, 77, 77, 77, 77, 17, 17, 17, 1, 16, 16] 77
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: 235
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071437 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071437
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071437/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071437
Building REAL250005071438
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071438'
/scratch/stefan/7916153/working/building/REAL250005071438 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071438

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071438/0 /scratch/stefan/7916153/working/building/REAL250005071438 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 568)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/568
`/scratch/stefan/7916153/working/3D/568' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1CCCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071438.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071438.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071438/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071438 none CN(C(=O)C1CCCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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, 19, 19, 38, 38, 38, 38, 1, 1, 1, 1, 5, 5, 18, 18, 18, 18, 18, 1, 7, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 18, 1, 1] 90
rigid atoms, others: [1, 34, 35, 37, 38, 33, 9, 10, 11, 12, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 134
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071438 none CN(C(=O)C1CCCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [22, 6, 1, 6, 1, 1, 1, 1, 1, 22, 38, 38, 38, 66, 66, 90, 90, 90, 90, 90, 38, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 90, 38, 38] 90
rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38])
total number of confs: 262
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071438 none CN(C(=O)C1CCCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [47, 19, 47, 68, 68, 90, 90, 90, 90, 19, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 47, 47, 47, 90, 90, 90, 90, 90, 90, 90, 90, 90, 19, 18, 18, 1, 19, 19] 90
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: 287
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071438 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071438
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071438/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071438
Building REAL250005071439
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071439'
/scratch/stefan/7916153/working/building/REAL250005071439 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071439

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071439/0 /scratch/stefan/7916153/working/building/REAL250005071439 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 569)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/569
`/scratch/stefan/7916153/working/3D/569' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071439.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071439.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071439/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071439 none C=CCCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 115, 97, 36, 21, 36, 8, 21, 8, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 201, 201, 201, 194, 194, 128, 128, 97, 97, 21, 21, 21, 8, 7, 8, 1, 8, 8] 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: 931
number of broken/clashed sets: 78
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071439 none C=CCCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 149, 82, 65, 20, 9, 20, 1, 9, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 1, 168, 168, 168, 144, 144, 91, 91, 65, 65, 9, 9, 9, 1, 1, 1, 8, 1, 1] 201
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 787
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071439 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071439
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071439/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071439
Building REAL250005071440
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071440'
/scratch/stefan/7916153/working/building/REAL250005071440 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071440

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071440/0 /scratch/stefan/7916153/working/building/REAL250005071440 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 570)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/570
`/scratch/stefan/7916153/working/3D/570' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071440.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071440.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071440/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071440 none CCC(C)(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 139, 84, 139, 139, 68, 84, 26, 68, 26, 25, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 145, 145, 145, 145, 145, 139, 139, 139, 139, 139, 139, 68, 68, 68, 26, 25, 26, 1, 26, 26] 145
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: 541
number of broken/clashed sets: 145
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071440 none CCC(C)(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [59, 37, 15, 37, 37, 9, 15, 1, 9, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 59, 59, 59, 59, 59, 37, 37, 37, 37, 37, 37, 9, 9, 9, 1, 1, 1, 26, 1, 1] 145
rigid atoms, others: [35, 36, 37, 7, 40, 9, 10, 11, 12, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 312
number of broken/clashed sets: 145
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071440 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071440
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071440/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071440
Building REAL250005071441
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071441'
/scratch/stefan/7916153/working/building/REAL250005071441 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071441

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071441/0 /scratch/stefan/7916153/working/building/REAL250005071441 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 571)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/571
`/scratch/stefan/7916153/working/3D/571' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C(N)=O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071441.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071441.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071441/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071441 none CN(C(=O)C(N)=O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 8, 11, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
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: [91, 30, 91, 107, 107, 124, 126, 30, 29, 11, 1, 11, 1, 1, 1, 1, 1, 1, 29, 91, 91, 91, 126, 124, 30, 29, 29, 1, 30, 29] 126
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])
total number of confs: 355
number of broken/clashed sets: 51
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071441 none CN(C(=O)C(N)=O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 8, 11, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
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: [9, 1, 9, 20, 20, 49, 51, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 9, 9, 9, 51, 49, 1, 1, 1, 29, 1, 1] 126
rigid atoms, others: [1, 7, 8, 9, 10, 18, 24, 25, 26, 28, 29] set([0, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 27])
total number of confs: 182
number of broken/clashed sets: 51
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071441 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071441
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071441/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071441
Building REAL250005071442
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071442'
/scratch/stefan/7916153/working/building/REAL250005071442 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071442

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071442/0 /scratch/stefan/7916153/working/building/REAL250005071442 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 572)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/572
`/scratch/stefan/7916153/working/3D/572' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071442.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071442.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071442/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071442 none CC1CC1CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 87, 21, 7, 21, 1, 7, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 137, 137, 137, 137, 137, 137, 137, 87, 87, 7, 7, 7, 1, 1, 1, 16, 1, 1] 201
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 501
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071442 none CC1CC1CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 35, 35, 86, 86, 137, 137, 137, 195, 195, 201, 201, 201, 201, 201, 137, 2, 2, 2, 1, 1, 1, 1, 8, 8, 86, 86, 86, 137, 137, 137, 201, 137, 137] 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: 655
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071442 none CC1CC1CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 69, 35, 69, 16, 35, 16, 16, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 201, 201, 201, 201, 201, 201, 201, 167, 167, 35, 35, 35, 16, 16, 16, 1, 16, 16] 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: 719
number of broken/clashed sets: 37
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071442 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071442
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071442/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071442
Building REAL250005071443
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071443'
/scratch/stefan/7916153/working/building/REAL250005071443 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071443

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071443/0 /scratch/stefan/7916153/working/building/REAL250005071443 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 573)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/573
`/scratch/stefan/7916153/working/3D/573' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1)

`REAL250005071443.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071443.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071443/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071443 none CCC1(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 15, 15, 7, 15, 1, 7, 1, 1, 1, 1, 4, 4, 13, 13, 13, 13, 13, 1, 15, 15, 18, 18, 18, 18, 18, 8, 8, 8, 1, 1, 1, 13, 1, 1, 15, 15, 15, 15] 38
rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 35, 36, 37, 38])
total number of confs: 80
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071443 none CCC1(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 1, 1, 3, 3, 6, 6, 15, 15, 15, 30, 30, 36, 36, 36, 36, 36, 15, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 15, 15, 15, 36, 15, 15, 1, 1, 1, 1] 38
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: 120
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071443 none CCC1(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [38, 36, 36, 24, 36, 14, 24, 14, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 36, 36, 38, 38, 38, 38, 38, 24, 24, 24, 14, 14, 14, 1, 13, 13, 36, 36, 36, 36] 38
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: 106
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071443 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071443
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071443/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071443
Building REAL250005071444
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071444'
/scratch/stefan/7916153/working/building/REAL250005071444 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071444

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071444/0 /scratch/stefan/7916153/working/building/REAL250005071444 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 574)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/574
`/scratch/stefan/7916153/working/3D/574' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C(C)(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071444.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071444.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071444/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071444 none CN(C(=O)C(C)(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 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, 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]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [55, 27, 55, 62, 62, 62, 62, 62, 27, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 27, 55, 55, 55, 62, 62, 62, 62, 62, 62, 62, 62, 62, 27, 26, 26, 1, 27, 27] 62
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: 155
number of broken/clashed sets: 62
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071444 none CN(C(=O)C(C)(C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 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, 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]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 15, 15, 15, 15, 15, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 26, 1, 1] 62
rigid atoms, others: [32, 1, 34, 36, 37, 33, 8, 9, 10, 11, 19] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 79
number of broken/clashed sets: 62
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071444 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071444
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071444/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071444
Building REAL250005071445
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071445'
/scratch/stefan/7916153/working/building/REAL250005071445 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071445

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071445/0 /scratch/stefan/7916153/working/building/REAL250005071445 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 575)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/575
`/scratch/stefan/7916153/working/3D/575' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071445.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071445.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071445/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071445 none C=C(C)CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 179, 91, 53, 91, 19, 53, 19, 18, 5, 1, 5, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 201, 198, 198, 179, 179, 53, 53, 53, 19, 18, 19, 1, 19, 19] 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: 740
number of broken/clashed sets: 72
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071445 none C=C(C)CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 124, 164, 104, 27, 9, 27, 1, 9, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 165, 165, 165, 165, 165, 124, 124, 104, 104, 9, 9, 9, 1, 1, 1, 19, 1, 1] 201
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 657
number of broken/clashed sets: 72
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071445 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071445
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071445/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071445
Building REAL250005071446
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071446'
/scratch/stefan/7916153/working/building/REAL250005071446 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071446

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071446/0 /scratch/stefan/7916153/working/building/REAL250005071446 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 576)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/576
`/scratch/stefan/7916153/working/3D/576' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1(CF)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071446.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071446.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071446/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071446 none CN(C(=O)C1(CF)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 15, 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]
dock color type numbers: [7, 7, 7, 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, 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: [9, 1, 9, 27, 27, 32, 80, 32, 32, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 9, 9, 9, 80, 80, 32, 32, 32, 32, 1, 1, 1, 20, 1, 1] 124
rigid atoms, others: [32, 1, 34, 35, 9, 10, 11, 12, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 325
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071446 none CN(C(=O)C1(CF)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 15, 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]
dock color type numbers: [7, 7, 7, 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, 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: [10, 3, 1, 3, 1, 1, 10, 1, 1, 10, 32, 32, 32, 76, 76, 115, 115, 115, 115, 115, 32, 10, 10, 10, 10, 10, 1, 1, 1, 1, 32, 32, 32, 115, 32, 32] 124
rigid atoms, others: [2, 4, 5, 7, 8, 26, 27, 28, 29] set([0, 1, 3, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35])
total number of confs: 312
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071446 none CN(C(=O)C1(CF)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 15, 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]
dock color type numbers: [7, 7, 7, 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, 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: [69, 21, 69, 108, 108, 115, 124, 115, 115, 21, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 69, 69, 69, 124, 124, 115, 115, 115, 115, 21, 20, 20, 1, 21, 21] 124
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: 360
number of broken/clashed sets: 50
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071446 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071446
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071446/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071446
Building REAL250005071447
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071447'
/scratch/stefan/7916153/working/building/REAL250005071447 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071447

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071447/0 /scratch/stefan/7916153/working/building/REAL250005071447 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 577)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/577
`/scratch/stefan/7916153/working/3D/577' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071447.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071447.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071447/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071447 none CC(C)C(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 119, 131, 99, 119, 58, 99, 22, 58, 22, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 131, 131, 131, 131, 131, 131, 131, 119, 119, 119, 119, 58, 58, 58, 22, 21, 22, 1, 22, 22] 131
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: 449
number of broken/clashed sets: 70
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071447 none CC(C)C(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [73, 53, 73, 30, 53, 9, 30, 1, 9, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 73, 73, 73, 73, 73, 73, 73, 53, 53, 53, 53, 9, 9, 9, 1, 1, 1, 22, 1, 1] 131
rigid atoms, others: [35, 36, 37, 7, 40, 9, 10, 11, 12, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 341
number of broken/clashed sets: 70
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071447 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071447
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071447/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071447
Building REAL250005071448
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071448'
/scratch/stefan/7916153/working/building/REAL250005071448 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071448

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071448/0 /scratch/stefan/7916153/working/building/REAL250005071448 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 578)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/578
`/scratch/stefan/7916153/working/3D/578' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1C[C@H]1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071448.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071448.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071448/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071448 none CC[C@@H]1C[C@H]1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 7, 5, 5, 7, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
185  conformations in input
total number of sets (complete confs): 185
using faster count positions algorithm for large data
unique positions, atoms: [97, 66, 66, 66, 66, 22, 66, 7, 22, 1, 7, 1, 1, 1, 1, 4, 4, 24, 24, 24, 24, 24, 1, 97, 97, 97, 97, 97, 66, 66, 7, 7, 7, 1, 1, 1, 25, 1, 1] 185
rigid atoms, others: [33, 34, 35, 37, 38, 9, 11, 12, 13, 14, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 399
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071448 none CC[C@@H]1C[C@H]1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 7, 5, 5, 7, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
185  conformations in input
total number of sets (complete confs): 185
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 31, 31, 66, 66, 66, 103, 103, 173, 173, 173, 173, 173, 66, 3, 3, 3, 3, 3, 1, 1, 31, 31, 31, 66, 66, 66, 173, 66, 66] 185
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: 442
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071448 none CC[C@@H]1C[C@H]1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 7, 5, 5, 7, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
185  conformations in input
total number of sets (complete confs): 185
using faster count positions algorithm for large data
unique positions, atoms: [185, 173, 173, 173, 173, 117, 173, 64, 117, 25, 64, 25, 24, 11, 1, 11, 1, 1, 1, 1, 1, 1, 25, 185, 185, 185, 185, 185, 173, 173, 64, 64, 64, 25, 24, 25, 1, 25, 25] 185
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: 599
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071448 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071448
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071448/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071448
Building REAL250005071449
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071449'
/scratch/stefan/7916153/working/building/REAL250005071449 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071449

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071449/0 /scratch/stefan/7916153/working/building/REAL250005071449 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 579)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/579
`/scratch/stefan/7916153/working/3D/579' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1CC12CC2)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071449.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071449.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071449/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071449 none CN(C(=O)C1CC12CC2)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 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]
dock color type numbers: [7, 7, 7, 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, 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: [9, 1, 9, 22, 22, 64, 64, 64, 64, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 9, 9, 9, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 26, 1, 1] 132
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 213
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071449 none CN(C(=O)C1CC12CC2)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 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]
dock color type numbers: [7, 7, 7, 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, 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: [26, 8, 1, 8, 1, 1, 1, 1, 1, 26, 64, 64, 64, 115, 115, 132, 132, 132, 132, 132, 64, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 132, 64, 64] 132
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36])
total number of confs: 378
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071449 none CN(C(=O)C1CC12CC2)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 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]
dock color type numbers: [7, 7, 7, 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, 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: [57, 26, 57, 92, 92, 132, 132, 132, 132, 26, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 57, 57, 57, 132, 132, 132, 132, 132, 132, 132, 26, 26, 26, 1, 26, 26] 132
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: 386
number of broken/clashed sets: 33
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071449 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071449
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071449/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071449
Building REAL250005071450
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071450'
/scratch/stefan/7916153/working/building/REAL250005071450 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071450

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071450/0 /scratch/stefan/7916153/working/building/REAL250005071450 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 580)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/580
`/scratch/stefan/7916153/working/3D/580' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)[C@H]1CCCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071450.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071450.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071450/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071450 none CN(C(=O)[C@H]1CCCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', '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, 7, 5, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 19, 19, 38, 38, 38, 38, 38, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 21, 1, 9, 9, 9, 38, 38, 38, 38, 38, 38, 1, 1, 1, 21, 1, 1] 75
rigid atoms, others: [32, 1, 35, 36, 33, 10, 11, 12, 13, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 129
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071450 none CN(C(=O)[C@H]1CCCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', '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, 7, 5, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 38, 38, 38, 60, 60, 75, 75, 75, 75, 75, 38, 25, 25, 25, 1, 1, 1, 1, 1, 1, 38, 38, 38, 75, 38, 38] 75
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36])
total number of confs: 218
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071450 none CN(C(=O)[C@H]1CCCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', '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', '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, 7, 5, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [45, 21, 45, 60, 60, 75, 75, 75, 75, 75, 21, 21, 12, 1, 12, 1, 1, 1, 1, 1, 1, 21, 45, 45, 45, 75, 75, 75, 75, 75, 75, 21, 21, 21, 1, 21, 21] 75
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: 217
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071450 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071450
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071450/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071450
Building REAL250005071451
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071451'
/scratch/stefan/7916153/working/building/REAL250005071451 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071451

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071451/0 /scratch/stefan/7916153/working/building/REAL250005071451 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 581)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/581
`/scratch/stefan/7916153/working/3D/581' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CC1(C)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071451.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071451.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071451/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071451 none CN(C(=O)CC1(C)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 23, 23, 72, 110, 110, 110, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 7, 7, 7, 72, 72, 110, 110, 110, 110, 110, 110, 110, 1, 1, 1, 16, 1, 1] 166
rigid atoms, others: [1, 34, 35, 37, 38, 33, 9, 10, 11, 12, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 412
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071451 none CN(C(=O)CC1(C)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [62, 25, 8, 25, 1, 1, 1, 1, 1, 62, 110, 110, 110, 160, 160, 166, 166, 166, 166, 166, 110, 62, 62, 62, 8, 8, 2, 2, 2, 1, 1, 1, 1, 110, 110, 110, 166, 110, 110] 166
rigid atoms, others: [32, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38])
total number of confs: 559
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071451 none CN(C(=O)CC1(C)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [44, 16, 44, 78, 78, 148, 166, 166, 166, 16, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 44, 44, 44, 148, 148, 166, 166, 166, 166, 166, 166, 166, 16, 16, 16, 1, 16, 16] 166
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: 599
number of broken/clashed sets: 34
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071451 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071451
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071451/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071451
Building REAL250005071452
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071452'
/scratch/stefan/7916153/working/building/REAL250005071452 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071452

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071452/0 /scratch/stefan/7916153/working/building/REAL250005071452 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 582)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/582
`/scratch/stefan/7916153/working/3D/582' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1(C)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071452.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071452.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071452/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071452 none CN(C(=O)C1(C)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 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]
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]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 19, 19, 22, 22, 22, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 23, 1, 1] 60
rigid atoms, others: [32, 1, 34, 35, 8, 9, 10, 11, 19, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071452 none CN(C(=O)C1(C)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 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]
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]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [9, 3, 1, 3, 1, 1, 1, 1, 9, 22, 22, 22, 50, 50, 60, 60, 60, 60, 60, 22, 9, 9, 9, 2, 2, 2, 1, 1, 1, 1, 22, 22, 22, 60, 22, 22] 60
rigid atoms, others: [2, 4, 5, 6, 7, 26, 27, 28, 29] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35])
total number of confs: 168
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071452 none CN(C(=O)C1(C)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 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]
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]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [46, 23, 46, 56, 56, 60, 60, 60, 23, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 46, 46, 46, 60, 60, 60, 60, 60, 60, 60, 23, 22, 23, 1, 23, 23] 60
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: 163
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071452 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071452
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071452/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071452
Building REAL250005071453
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071453'
/scratch/stefan/7916153/working/building/REAL250005071453 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071453

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071453/0 /scratch/stefan/7916153/working/building/REAL250005071453 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 583)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/583
`/scratch/stefan/7916153/working/3D/583' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CNC=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071453.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071453.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071453/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071453 none CN(C(=O)C1=CNC=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 1, 1, 8, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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: [8, 1, 8, 24, 24, 81, 81, 81, 81, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 8, 8, 8, 81, 81, 81, 81, 1, 1, 1, 29, 1, 1] 153
rigid atoms, others: [32, 1, 33, 9, 10, 11, 12, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 180
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071453 none CN(C(=O)C1=CNC=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 1, 1, 8, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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: [36, 11, 1, 11, 1, 1, 1, 1, 1, 36, 81, 81, 81, 133, 133, 153, 153, 153, 153, 153, 81, 36, 36, 36, 1, 1, 1, 1, 81, 81, 81, 153, 81, 81] 153
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33])
total number of confs: 448
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071453 none CN(C(=O)C1=CNC=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 1, 1, 8, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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: [67, 29, 67, 102, 102, 153, 153, 153, 153, 29, 29, 11, 1, 11, 1, 1, 1, 1, 1, 1, 29, 67, 67, 67, 153, 153, 153, 153, 29, 29, 29, 1, 29, 29] 153
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])
total number of confs: 375
number of broken/clashed sets: 31
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071453 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071453
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071453/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071453
Building REAL250005071454
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071454'
/scratch/stefan/7916153/working/building/REAL250005071454 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071454

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071454/0 /scratch/stefan/7916153/working/building/REAL250005071454 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 584)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/584
`/scratch/stefan/7916153/working/3D/584' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CN=CO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071454.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071454.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071454/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071454 none CN(C(=O)C1=CN=CO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 6, 7, 7, 7, 3, 7, 3, 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: [6, 1, 6, 20, 20, 37, 37, 37, 37, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 7, 7, 7, 37, 37, 1, 1, 1, 18, 1, 1] 67
rigid atoms, others: [1, 9, 10, 11, 12, 20, 26, 27, 28, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29])
total number of confs: 109
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071454 none CN(C(=O)C1=CN=CO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 6, 7, 7, 7, 3, 7, 3, 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: [22, 10, 1, 10, 1, 1, 1, 1, 1, 22, 37, 37, 37, 62, 62, 67, 67, 67, 67, 67, 37, 22, 22, 22, 1, 1, 37, 37, 37, 67, 37, 37] 67
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 209
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071454 none CN(C(=O)C1=CN=CO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 6, 7, 7, 7, 3, 7, 3, 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: [34, 18, 34, 52, 52, 67, 67, 67, 67, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 34, 34, 34, 67, 67, 18, 18, 18, 1, 18, 18] 67
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 160
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071454 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071454
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071454/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071454
Building REAL250005071455
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071455'
/scratch/stefan/7916153/working/building/REAL250005071455 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071455

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071455/0 /scratch/stefan/7916153/working/building/REAL250005071455 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 585)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/585
`/scratch/stefan/7916153/working/3D/585' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(C)(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071455.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071455.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071455/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071455 none C=CC(C)(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 57, 57, 57, 49, 57, 21, 49, 21, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 57, 57, 57, 57, 57, 57, 57, 57, 57, 49, 49, 49, 21, 20, 21, 1, 21, 21] 57
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: 141
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071455 none C=CC(C)(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 15, 15, 15, 9, 15, 1, 9, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 22, 22, 22, 15, 15, 15, 15, 15, 15, 9, 9, 9, 1, 1, 1, 21, 1, 1] 57
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 101
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071455 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071455
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071455/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071455
Building REAL250005071456
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071456'
/scratch/stefan/7916153/working/building/REAL250005071456 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071456

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071456/0 /scratch/stefan/7916153/working/building/REAL250005071456 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 586)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/586
`/scratch/stefan/7916153/working/3D/586' -> `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)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071456.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071456.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071456/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071456 none C[C@@H]1C[C@H]1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [42, 42, 42, 42, 16, 42, 7, 16, 1, 7, 1, 1, 1, 1, 5, 5, 18, 18, 18, 18, 18, 1, 42, 42, 42, 42, 42, 7, 7, 7, 1, 1, 1, 18, 1, 1] 73
rigid atoms, others: [32, 34, 35, 8, 10, 11, 12, 13, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 141
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071456 none C[C@@H]1C[C@H]1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 26, 42, 42, 42, 66, 66, 73, 73, 73, 73, 73, 42, 2, 2, 2, 1, 1, 26, 26, 26, 42, 42, 42, 73, 42, 42] 73
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: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071456 none C[C@@H]1C[C@H]1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 73, 57, 73, 43, 57, 18, 43, 18, 18, 10, 1, 10, 1, 1, 1, 1, 1, 1, 18, 73, 73, 73, 73, 73, 43, 43, 43, 18, 18, 18, 1, 18, 18] 73
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: 216
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071456 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071456
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071456/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071456
Building REAL250005071457
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071457'
/scratch/stefan/7916153/working/building/REAL250005071457 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071457

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071457/0 /scratch/stefan/7916153/working/building/REAL250005071457 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 587)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/587
`/scratch/stefan/7916153/working/3D/587' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1(C)CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071457.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071457.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071457/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071457 none CN(C(=O)C1(C)CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [9, 1, 9, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 1, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 13, 1, 1] 34
rigid atoms, others: [1, 34, 35, 37, 38, 33, 9, 10, 11, 12, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 64
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071457 none CN(C(=O)C1(C)CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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, 3, 1, 3, 1, 1, 1, 1, 1, 6, 18, 18, 18, 31, 31, 34, 34, 34, 34, 34, 17, 6, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 34, 18, 18] 34
rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 27, 28, 29, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36, 37, 38])
total number of confs: 109
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071457 none CN(C(=O)C1(C)CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [25, 14, 25, 34, 34, 34, 34, 34, 34, 14, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 25, 25, 25, 34, 34, 34, 34, 34, 34, 34, 34, 34, 14, 13, 13, 1, 14, 14] 34
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: 84
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071457 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071457
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071457/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071457
Building REAL250005071458
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071458'
/scratch/stefan/7916153/working/building/REAL250005071458 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071458

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071458/0 /scratch/stefan/7916153/working/building/REAL250005071458 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 588)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/588
`/scratch/stefan/7916153/working/3D/588' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071458.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071458.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071458/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071458 none CCC(F)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [182, 175, 119, 175, 77, 119, 27, 77, 27, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 182, 182, 182, 182, 182, 175, 77, 77, 77, 27, 26, 27, 1, 27, 27] 182
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: 624
number of broken/clashed sets: 80
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071458 none CCC(F)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [110, 88, 28, 88, 9, 28, 1, 9, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 114, 114, 114, 114, 114, 88, 9, 9, 9, 1, 1, 1, 27, 1, 1] 182
rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 536
number of broken/clashed sets: 80
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071458 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071458
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071458/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071458
Building REAL250005071459
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071459'
/scratch/stefan/7916153/working/building/REAL250005071459 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071459

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071459/0 /scratch/stefan/7916153/working/building/REAL250005071459 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 589)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/589
`/scratch/stefan/7916153/working/3D/589' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CCCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071459.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071459.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071459/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071459 none CN(C(=O)CCCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', '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, 5, 5, 15, 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]
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]
0  hydrogens 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, 12, 42, 80, 80, 166, 192, 201, 12, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 42, 42, 42, 166, 166, 201, 201, 201, 201, 12, 11, 12, 1, 12, 12] 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: 848
number of broken/clashed sets: 87
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071459 none CN(C(=O)CCCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', '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, 5, 5, 15, 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]
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]
0  hydrogens 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, 24, 24, 78, 95, 150, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 1, 9, 9, 9, 78, 78, 105, 105, 147, 149, 1, 1, 1, 12, 1, 1] 201
rigid atoms, others: [1, 34, 33, 8, 9, 10, 11, 19, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 757
number of broken/clashed sets: 87
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071459 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071459
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071459/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071459
Building REAL250005071460
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071460'
/scratch/stefan/7916153/working/building/REAL250005071460 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071460

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071460/0 /scratch/stefan/7916153/working/building/REAL250005071460 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 590)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/590
`/scratch/stefan/7916153/working/3D/590' -> `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)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071460.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071460.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071460/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071460 none C[C@H]1C[C@@H]1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 71, 29, 71, 9, 29, 1, 9, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 71, 71, 71, 71, 71, 9, 9, 9, 1, 1, 1, 21, 1, 1] 138
rigid atoms, others: [32, 34, 35, 8, 10, 11, 12, 13, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 226
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071460 none C[C@H]1C[C@@H]1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 30, 30, 71, 71, 71, 126, 126, 138, 138, 138, 138, 138, 71, 2, 2, 2, 1, 1, 30, 30, 30, 71, 71, 71, 138, 71, 71] 138
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: 399
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071460 none C[C@H]1C[C@@H]1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [138, 138, 138, 138, 110, 138, 75, 110, 21, 75, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 138, 138, 138, 138, 138, 75, 75, 75, 21, 21, 21, 1, 21, 21] 138
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: 407
number of broken/clashed sets: 67
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071460 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071460
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071460/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071460
Building REAL250005071461
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071461'
/scratch/stefan/7916153/working/building/REAL250005071461 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071461

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071461/0 /scratch/stefan/7916153/working/building/REAL250005071461 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 591)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/591
`/scratch/stefan/7916153/working/3D/591' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(F)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071461.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071461.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071461/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071461 none CC(C)C(F)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 15, 1, 11, 8, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 167, 201, 109, 167, 63, 109, 21, 63, 21, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 201, 201, 201, 201, 201, 201, 201, 167, 63, 63, 63, 21, 20, 20, 1, 21, 21] 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: 770
number of broken/clashed sets: 98
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071461 none CC(C)C(F)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 15, 1, 11, 8, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [124, 92, 124, 33, 92, 9, 33, 1, 9, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 124, 124, 124, 124, 124, 124, 124, 92, 9, 9, 9, 1, 1, 1, 20, 1, 1] 201
rigid atoms, others: [32, 33, 34, 36, 37, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 529
number of broken/clashed sets: 98
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071461 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071461
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071461/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071461
Building REAL250005071462
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071462'
/scratch/stefan/7916153/working/building/REAL250005071462 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071462

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071462/0 /scratch/stefan/7916153/working/building/REAL250005071462 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 592)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/592
`/scratch/stefan/7916153/working/3D/592' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=NNN=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071462.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071462.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071462/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071462 none CN(C(=O)C1=NNN=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 8, 8, 8, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
0  hydrogens need rotated
147  conformations in input
total number of sets (complete confs): 147
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 31, 31, 79, 79, 79, 79, 1, 1, 1, 1, 6, 6, 25, 25, 26, 25, 25, 1, 9, 9, 9, 79, 79, 1, 1, 1, 26, 1, 1] 147
rigid atoms, others: [1, 9, 10, 11, 12, 20, 26, 27, 28, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29])
total number of confs: 184
number of broken/clashed sets: 68
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071462 none CN(C(=O)C1=NNN=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 8, 8, 8, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
0  hydrogens need rotated
147  conformations in input
total number of sets (complete confs): 147
using faster count positions algorithm for large data
unique positions, atoms: [31, 10, 1, 10, 1, 1, 1, 1, 1, 31, 79, 79, 79, 136, 136, 147, 147, 147, 147, 147, 79, 31, 31, 31, 1, 1, 79, 79, 79, 147, 79, 79] 147
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 437
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071462 none CN(C(=O)C1=NNN=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 8, 8, 8, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
0  hydrogens need rotated
147  conformations in input
total number of sets (complete confs): 147
using faster count positions algorithm for large data
unique positions, atoms: [84, 26, 84, 130, 130, 147, 147, 147, 147, 26, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 84, 84, 84, 147, 147, 26, 25, 26, 1, 26, 25] 147
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 377
number of broken/clashed sets: 68
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071462 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071462
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071462/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071462
Building REAL250005071463
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071463'
/scratch/stefan/7916153/working/building/REAL250005071463 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071463

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071463/0 /scratch/stefan/7916153/working/building/REAL250005071463 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 593)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/593
`/scratch/stefan/7916153/working/3D/593' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071463.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071463.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071463/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071463 none CN(C(=O)CO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
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: [87, 30, 87, 116, 116, 130, 30, 29, 11, 1, 11, 1, 1, 1, 1, 1, 1, 30, 87, 87, 87, 130, 130, 390, 30, 29, 30, 1, 30, 30] 390
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])
total number of confs: 794
number of broken/clashed sets: 201
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071463 none CN(C(=O)CO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 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]
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: [9, 1, 9, 27, 27, 67, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 9, 9, 9, 67, 67, 201, 1, 1, 1, 30, 1, 1] 390
rigid atoms, others: [1, 6, 7, 8, 9, 17, 24, 25, 26, 28, 29] set([0, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 27])
total number of confs: 485
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071463 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071463
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071463/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071463
Building REAL250005071464
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071464'
/scratch/stefan/7916153/working/building/REAL250005071464 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071464

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071464/0 /scratch/stefan/7916153/working/building/REAL250005071464 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 594)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/594
`/scratch/stefan/7916153/working/3D/594' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C=CC(N)=O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071464.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071464.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071464/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071464 none CN(C(=O)C=CC(N)=O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 8, 11, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 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, 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: [34, 15, 34, 41, 41, 50, 50, 54, 54, 15, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 34, 34, 34, 50, 50, 54, 54, 15, 14, 15, 1, 15, 15] 54
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])
total number of confs: 155
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071464 none CN(C(=O)C=CC(N)=O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 8, 11, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 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, 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: [9, 1, 9, 15, 15, 32, 32, 42, 42, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 14, 1, 9, 9, 9, 32, 32, 42, 42, 1, 1, 1, 15, 1, 1] 54
rigid atoms, others: [32, 1, 33, 9, 10, 11, 12, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 146
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071464 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071464
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071464/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071464
Building REAL250005071465
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071465'
/scratch/stefan/7916153/working/building/REAL250005071465 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071465

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071465/0 /scratch/stefan/7916153/working/building/REAL250005071465 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 595)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/595
`/scratch/stefan/7916153/working/3D/595' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071465.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071465.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071465/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071465 none COC(=O)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 5, 1, 11, 8, 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]
dock color type numbers: [7, 3, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 53, 35, 53, 9, 35, 9, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 201, 201, 201, 141, 141, 35, 35, 35, 9, 8, 9, 1, 9, 9] 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: 741
number of broken/clashed sets: 107
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071465 none COC(=O)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 5, 1, 11, 8, 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]
dock color type numbers: [7, 3, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 75, 158, 18, 9, 18, 1, 9, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 1, 158, 158, 158, 75, 75, 9, 9, 9, 1, 1, 1, 9, 1, 1] 201
rigid atoms, others: [33, 34, 7, 9, 10, 11, 12, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 538
number of broken/clashed sets: 107
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071465 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071465
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071465/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071465
Building REAL250005071466
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071466'
/scratch/stefan/7916153/working/building/REAL250005071466 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071466

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071466/0 /scratch/stefan/7916153/working/building/REAL250005071466 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 596)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/596
`/scratch/stefan/7916153/working/3D/596' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071466.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071466.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071466/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071466 none CSC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.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', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 185, 185, 106, 61, 106, 20, 61, 20, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 201, 201, 201, 185, 185, 61, 61, 61, 20, 19, 20, 1, 20, 20] 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])
total number of confs: 573
number of broken/clashed sets: 76
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071466 none CSC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.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', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 101, 101, 29, 9, 29, 1, 9, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 164, 164, 164, 101, 101, 9, 9, 9, 1, 1, 1, 20, 1, 1] 201
rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 389
number of broken/clashed sets: 76
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071466 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071466
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071466/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071466
Building REAL250005071467
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071467'
/scratch/stefan/7916153/working/building/REAL250005071467 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071467

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071467/0 /scratch/stefan/7916153/working/building/REAL250005071467 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 597)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/597
`/scratch/stefan/7916153/working/3D/597' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CCC(N)=O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071467.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071467.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071467/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071467 none CN(C(=O)CCC(N)=O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', '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, 5, 1, 8, 11, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 11, 41, 72, 72, 141, 169, 201, 201, 11, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 41, 41, 41, 141, 141, 169, 169, 201, 201, 11, 10, 11, 1, 11, 11] 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: 762
number of broken/clashed sets: 87
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071467 none CN(C(=O)CCC(N)=O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', '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, 5, 1, 8, 11, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 25, 25, 77, 105, 164, 164, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 1, 9, 9, 9, 77, 77, 105, 105, 164, 164, 1, 1, 1, 11, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 9, 10, 11, 12, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 633
number of broken/clashed sets: 87
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071467 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071467
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071467/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071467
Building REAL250005071468
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071468'
/scratch/stefan/7916153/working/building/REAL250005071468 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071468

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071468/0 /scratch/stefan/7916153/working/building/REAL250005071468 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 598)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/598
`/scratch/stefan/7916153/working/3D/598' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1CCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071468.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071468.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071468/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071468 none CN(C(=O)C1CCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 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
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [8, 1, 8, 15, 15, 31, 31, 31, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 14, 1, 9, 9, 9, 31, 31, 31, 31, 31, 1, 1, 1, 14, 1, 1] 48
rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 19, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 31])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071468 none CN(C(=O)C1CCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 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
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [18, 6, 1, 6, 1, 1, 1, 1, 18, 31, 31, 31, 43, 43, 48, 48, 48, 48, 48, 31, 18, 18, 18, 1, 1, 1, 1, 1, 31, 31, 31, 48, 31, 31] 48
rigid atoms, others: [2, 4, 5, 6, 7, 23, 24, 25, 26, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33])
total number of confs: 146
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071468 none CN(C(=O)C1CCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 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
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [29, 15, 29, 39, 39, 48, 48, 48, 15, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 29, 29, 29, 48, 48, 48, 48, 48, 15, 15, 15, 1, 14, 14] 48
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: 138
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071468 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071468
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071468/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071468
Building REAL250005071469
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071469'
/scratch/stefan/7916153/working/building/REAL250005071469 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071469

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071469/0 /scratch/stefan/7916153/working/building/REAL250005071469 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 599)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/599
`/scratch/stefan/7916153/working/3D/599' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1(Cl)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071469.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071469.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071469/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071469 none CN(C(=O)C1(Cl)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 5, 16, 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]
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]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 19, 19, 34, 34, 34, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 1, 9, 9, 9, 34, 34, 34, 34, 1, 1, 1, 17, 1, 1] 81
rigid atoms, others: [32, 1, 8, 9, 10, 11, 19, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 133
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071469 none CN(C(=O)C1(Cl)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 5, 16, 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]
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]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [13, 7, 1, 7, 1, 1, 1, 1, 13, 34, 34, 34, 68, 68, 81, 81, 81, 81, 81, 34, 13, 13, 13, 1, 1, 1, 1, 34, 34, 34, 81, 34, 34] 81
rigid atoms, others: [2, 4, 5, 6, 7, 23, 24, 25, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32])
total number of confs: 238
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071469 none CN(C(=O)C1(Cl)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 5, 16, 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]
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]
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: [40, 17, 40, 61, 61, 81, 81, 81, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 40, 40, 40, 81, 81, 81, 81, 17, 17, 17, 1, 17, 17] 81
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: 245
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071469 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071469
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071469/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071469
Building REAL250005071470
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071470'
/scratch/stefan/7916153/working/building/REAL250005071470 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071470

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071470/0 /scratch/stefan/7916153/working/building/REAL250005071470 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 600)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/600
`/scratch/stefan/7916153/working/3D/600' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CCCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071470.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071470.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071470/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071470 none CN(C(=O)C1=CCCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 21, 21, 55, 55, 55, 55, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 7, 7, 7, 55, 55, 55, 55, 55, 1, 1, 1, 23, 1, 1] 85
rigid atoms, others: [1, 34, 33, 9, 10, 11, 12, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 139
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071470 none CN(C(=O)C1=CCCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [33, 10, 1, 10, 1, 1, 1, 1, 1, 33, 55, 55, 55, 80, 80, 85, 85, 85, 85, 85, 55, 33, 33, 33, 1, 1, 1, 1, 1, 55, 55, 55, 85, 55, 55] 85
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34])
total number of confs: 252
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071470 none CN(C(=O)C1=CCCO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [44, 23, 44, 67, 67, 85, 85, 85, 85, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 44, 44, 44, 85, 85, 85, 85, 85, 23, 23, 23, 1, 23, 23] 85
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: 202
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071470 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071470
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071470/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071470
Building REAL250005071471
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071471'
/scratch/stefan/7916153/working/building/REAL250005071471 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071471

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071471/0 /scratch/stefan/7916153/working/building/REAL250005071471 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 601)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/601
`/scratch/stefan/7916153/working/3D/601' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1COC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071471.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071471.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071471/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071471 none CN(C(=O)C1COC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 8, 1, 11, 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]
dock color type numbers: [7, 7, 7, 6, 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]
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: [9, 1, 9, 24, 24, 58, 58, 58, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 9, 9, 9, 58, 58, 58, 58, 58, 1, 1, 1, 25, 1, 1] 121
rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 19, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 195
number of broken/clashed sets: 47
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071471 none CN(C(=O)C1COC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 8, 1, 11, 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]
dock color type numbers: [7, 7, 7, 6, 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]
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: [21, 7, 1, 7, 1, 1, 1, 1, 21, 58, 58, 58, 109, 109, 121, 121, 121, 121, 121, 58, 21, 21, 21, 1, 1, 1, 1, 1, 58, 58, 58, 121, 58, 58] 121
rigid atoms, others: [2, 4, 5, 6, 7, 23, 24, 25, 26, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33])
total number of confs: 343
number of broken/clashed sets: 47
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071471 none CN(C(=O)C1COC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 8, 1, 11, 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]
dock color type numbers: [7, 7, 7, 6, 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]
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: [74, 25, 74, 93, 93, 121, 121, 121, 25, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 74, 74, 74, 121, 121, 121, 121, 121, 25, 24, 25, 1, 25, 25] 121
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: 357
number of broken/clashed sets: 47
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071471 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071471
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071471/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071471
Building REAL250005071472
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071472'
/scratch/stefan/7916153/working/building/REAL250005071472 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071472

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071472/0 /scratch/stefan/7916153/working/building/REAL250005071472 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 602)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/602
`/scratch/stefan/7916153/working/3D/602' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C=CCO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071472.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071472.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071472/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071472 none CN(C(=O)C=CCO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 5, 12, 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]
dock color type numbers: [7, 7, 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
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [70, 21, 70, 118, 118, 191, 191, 201, 21, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 21, 70, 70, 70, 191, 191, 201, 201, 603, 21, 20, 21, 1, 21, 21] 603
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: 1207
number of broken/clashed sets: 222
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071472 none CN(C(=O)C=CCO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 5, 12, 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]
dock color type numbers: [7, 7, 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
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 25, 25, 103, 103, 173, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 9, 9, 9, 103, 103, 173, 173, 519, 1, 1, 1, 21, 1, 1] 603
rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 19, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 1169
number of broken/clashed sets: 222
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071472 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071472
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071472/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071472
Building REAL250005071473
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071473'
/scratch/stefan/7916153/working/building/REAL250005071473 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071473

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071473/0 /scratch/stefan/7916153/working/building/REAL250005071473 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 603)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/603
`/scratch/stefan/7916153/working/3D/603' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071473.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071473.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071473/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071473 none CC=CC(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
564  conformations in input
total number of sets (complete confs): 564
using faster count positions algorithm for large data
unique positions, atoms: [188, 188, 153, 104, 153, 57, 104, 17, 57, 17, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 188, 188, 188, 188, 188, 153, 459, 57, 57, 57, 17, 16, 17, 1, 17, 17] 564
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: 1138
number of broken/clashed sets: 289
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071473 none CC=CC(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
564  conformations in input
total number of sets (complete confs): 564
using faster count positions algorithm for large data
unique positions, atoms: [132, 132, 65, 27, 65, 9, 27, 1, 9, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 132, 132, 132, 132, 132, 65, 195, 9, 9, 9, 1, 1, 1, 17, 1, 1] 564
rigid atoms, others: [32, 33, 35, 36, 7, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 682
number of broken/clashed sets: 289
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071473 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071473
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071473/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071473
Building REAL250005071474
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071474'
/scratch/stefan/7916153/working/building/REAL250005071474 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071474

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071474/0 /scratch/stefan/7916153/working/building/REAL250005071474 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 604)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/604
`/scratch/stefan/7916153/working/3D/604' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C)

`REAL250005071474.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071474.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071474/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071474 none C[C@@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 7, 3, 7, 3, 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
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 16, 20, 7, 16, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 20, 21, 21, 21, 20, 20, 20, 16, 16, 16, 7, 7, 7, 1, 7, 7, 21, 21, 21, 21, 21, 21] 21
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, 39, 40])
total number of confs: 57
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071474 none C[C@@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 7, 3, 7, 3, 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
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [12, 10, 12, 7, 10, 1, 7, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 1, 12, 14, 14, 14, 12, 12, 12, 7, 7, 7, 1, 1, 1, 7, 1, 1, 14, 14, 14, 14, 14, 14] 21
rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 65
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071474 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071474/1 /scratch/stefan/7916153/working/building/REAL250005071474 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 605)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/605
`/scratch/stefan/7916153/working/3D/605' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C)

`REAL250005071474.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071474.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071474/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071474 none C[C@@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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: [130, 107, 130, 63, 107, 18, 63, 18, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 130, 133, 133, 130, 130, 130, 63, 63, 63, 18, 17, 18, 1, 18, 18, 133, 133, 133, 133, 133, 133] 133
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, 39])
total number of confs: 426
number of broken/clashed sets: 69
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071474 none C[C@@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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: [66, 29, 66, 9, 29, 1, 9, 1, 1, 1, 1, 6, 6, 17, 17, 17, 18, 18, 1, 66, 82, 82, 66, 66, 66, 9, 9, 9, 1, 1, 1, 18, 1, 1, 82, 82, 82, 82, 82, 82] 133
rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 341
number of broken/clashed sets: 69
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071474 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071474
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071474/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071474/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071474
Building REAL250005071475
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071475'
/scratch/stefan/7916153/working/building/REAL250005071475 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071475

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071475/0 /scratch/stefan/7916153/working/building/REAL250005071475 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 606)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/606
`/scratch/stefan/7916153/working/3D/606' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=C(F)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071475.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071475.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071475/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071475 none CCC=C(F)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 15, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 141, 141, 76, 141, 42, 76, 16, 42, 16, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 201, 201, 201, 201, 201, 141, 42, 42, 42, 16, 15, 15, 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: 769
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071475 none CCC=C(F)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 15, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [150, 89, 89, 28, 89, 9, 28, 1, 9, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 150, 150, 150, 150, 150, 89, 9, 9, 9, 1, 1, 1, 15, 1, 1] 201
rigid atoms, others: [32, 34, 35, 7, 9, 10, 11, 12, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 595
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071475 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071475
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071475/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071475
Building REAL250005071476
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071476'
/scratch/stefan/7916153/working/building/REAL250005071476 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071476

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071476/0 /scratch/stefan/7916153/working/building/REAL250005071476 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 607)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/607
`/scratch/stefan/7916153/working/3D/607' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071476.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071476.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071476/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071476 none CCC=CC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 112, 64, 112, 20, 64, 20, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 201, 201, 201, 201, 201, 163, 163, 64, 64, 64, 20, 19, 20, 1, 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])
total number of confs: 714
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071476 none CCC=CC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 92, 92, 32, 9, 32, 1, 9, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 145, 145, 145, 145, 145, 92, 92, 9, 9, 9, 1, 1, 1, 20, 1, 1] 201
rigid atoms, others: [32, 34, 35, 6, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 574
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071476 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071476
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071476/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071476
Building REAL250005071477
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071477'
/scratch/stefan/7916153/working/building/REAL250005071477 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071477

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071477/0 /scratch/stefan/7916153/working/building/REAL250005071477 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 608)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/608
`/scratch/stefan/7916153/working/3D/608' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CCN=[N+]=[N-])C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071477.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071477.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071477/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071477 none CN(C(=O)CCN=[N+]=[N-])C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 8, 8, 8, 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]
dock color type numbers: [7, 7, 7, 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]
0  hydrogens 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, 16, 45, 67, 67, 126, 130, 201, 201, 16, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 45, 45, 45, 126, 126, 130, 130, 16, 15, 16, 1, 16, 16] 201
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])
total number of confs: 575
number of broken/clashed sets: 78
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071477 none CN(C(=O)CCN=[N+]=[N-])C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 8, 8, 8, 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]
dock color type numbers: [7, 7, 7, 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]
0  hydrogens 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, 22, 22, 72, 79, 163, 163, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 9, 9, 9, 72, 72, 79, 79, 1, 1, 1, 16, 1, 1] 201
rigid atoms, others: [32, 1, 33, 9, 10, 11, 12, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 455
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071477 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071477
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071477/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071477
Building REAL250005071478
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071478'
/scratch/stefan/7916153/working/building/REAL250005071478 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071478

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071478/0 /scratch/stefan/7916153/working/building/REAL250005071478 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 609)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/609
`/scratch/stefan/7916153/working/3D/609' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCOCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071478.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071478.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071478/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071478 none C#CCOCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 101, 52, 37, 52, 12, 37, 12, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 101, 101, 37, 37, 37, 12, 11, 12, 1, 12, 12] 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: 699
number of broken/clashed sets: 76
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071478 none C#CCOCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 94, 45, 16, 9, 16, 1, 9, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 1, 153, 153, 153, 45, 45, 9, 9, 9, 1, 1, 1, 12, 1, 1] 201
rigid atoms, others: [33, 34, 7, 9, 10, 11, 12, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 559
number of broken/clashed sets: 76
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071478 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071478
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071478/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071478
Building REAL250005071479
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071479'
/scratch/stefan/7916153/working/building/REAL250005071479 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071479

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071479/0 /scratch/stefan/7916153/working/building/REAL250005071479 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 610)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/610
`/scratch/stefan/7916153/working/3D/610' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071479.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071479.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071479/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071479 none CC(O)CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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, 139, 201, 130, 62, 37, 62, 14, 37, 14, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 190, 603, 150, 150, 130, 130, 37, 37, 37, 14, 13, 14, 1, 14, 14] 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: 1470
number of broken/clashed sets: 254
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071479 none CC(O)CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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: [152, 90, 152, 77, 24, 9, 24, 1, 9, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 152, 152, 152, 144, 456, 99, 99, 77, 77, 9, 9, 9, 1, 1, 1, 14, 1, 1] 603
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 1167
number of broken/clashed sets: 254
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071479 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071479
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071479/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071479
Building REAL250005071480
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071480'
/scratch/stefan/7916153/working/building/REAL250005071480 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071480

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071480/0 /scratch/stefan/7916153/working/building/REAL250005071480 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 611)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/611
`/scratch/stefan/7916153/working/3D/611' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071480.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071480.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071480/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071480 none C#CCCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 185, 112, 72, 112, 24, 72, 24, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 200, 200, 200, 185, 185, 72, 72, 72, 24, 23, 24, 1, 24, 24] 200
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: 722
number of broken/clashed sets: 87
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071480 none C#CCCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [128, 128, 97, 28, 9, 28, 1, 9, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 128, 128, 128, 97, 97, 9, 9, 9, 1, 1, 1, 24, 1, 1] 200
rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 556
number of broken/clashed sets: 87
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071480 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071480
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071480/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071480
Building REAL250005071481
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071481'
/scratch/stefan/7916153/working/building/REAL250005071481 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071481

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071481/0 /scratch/stefan/7916153/working/building/REAL250005071481 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 612)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/612
`/scratch/stefan/7916153/working/3D/612' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071481.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071481.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071481/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071481 none CC=CC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 191, 191, 132, 77, 132, 24, 77, 24, 23, 7, 1, 7, 1, 1, 1, 1, 1, 1, 24, 201, 201, 201, 201, 201, 191, 191, 77, 77, 77, 24, 23, 24, 1, 24, 24] 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: 600
number of broken/clashed sets: 75
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071481 none CC=CC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 94, 94, 27, 9, 27, 1, 9, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 123, 123, 123, 123, 123, 94, 94, 9, 9, 9, 1, 1, 1, 24, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 7, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 400
number of broken/clashed sets: 75
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071481 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071481
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071481/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071481
Building REAL250005071482
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071482'
/scratch/stefan/7916153/working/building/REAL250005071482 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071482

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071482/0 /scratch/stefan/7916153/working/building/REAL250005071482 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 613)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/613
`/scratch/stefan/7916153/working/3D/613' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071482.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071482.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071482/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071482 none COCC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 11, 8, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 126, 126, 54, 33, 54, 11, 33, 11, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 201, 201, 201, 197, 197, 126, 126, 33, 33, 33, 11, 10, 11, 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: 717
number of broken/clashed sets: 69
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071482 none COCC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 11, 8, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [185, 167, 75, 75, 22, 9, 22, 1, 9, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 1, 185, 185, 185, 167, 167, 75, 75, 9, 9, 9, 1, 1, 1, 11, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 7, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 681
number of broken/clashed sets: 69
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071482 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071482
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071482/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071482
Building REAL250005071483
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071483'
/scratch/stefan/7916153/working/building/REAL250005071483 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071483

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071483/0 /scratch/stefan/7916153/working/building/REAL250005071483 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 614)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/614
`/scratch/stefan/7916153/working/3D/614' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071483.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071483.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071483/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071483 none CCC(C)(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [78, 73, 73, 73, 73, 54, 73, 22, 54, 22, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 78, 78, 78, 78, 78, 73, 73, 73, 219, 54, 54, 54, 22, 21, 22, 1, 22, 22] 234
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: 433
number of broken/clashed sets: 138
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071483 none CCC(C)(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 20, 20, 20, 20, 9, 20, 1, 9, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 32, 32, 32, 32, 32, 20, 20, 20, 60, 9, 9, 9, 1, 1, 1, 22, 1, 1] 234
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 213
number of broken/clashed sets: 138
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071483 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071483
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071483/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071483
Building REAL250005071484
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071484'
/scratch/stefan/7916153/working/building/REAL250005071484 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071484

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071484/0 /scratch/stefan/7916153/working/building/REAL250005071484 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 615)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/615
`/scratch/stefan/7916153/working/3D/615' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071484.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071484.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071484/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071484 none C#CCC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 166, 103, 166, 57, 103, 18, 57, 18, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 201, 201, 201, 166, 166, 166, 166, 57, 57, 57, 18, 17, 17, 1, 18, 18] 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: 816
number of broken/clashed sets: 98
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071484 none C#CCC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [133, 133, 73, 31, 73, 9, 31, 1, 9, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 133, 133, 133, 73, 73, 73, 73, 9, 9, 9, 1, 1, 1, 17, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 7, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 599
number of broken/clashed sets: 98
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071484 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071484
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071484/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071484
Building REAL250005071485
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071485'
/scratch/stefan/7916153/working/building/REAL250005071485 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071485

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071485/0 /scratch/stefan/7916153/working/building/REAL250005071485 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 616)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/616
`/scratch/stefan/7916153/working/3D/616' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071485.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071485.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071485/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071485 none C=CC(O)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
414  conformations in input
total number of sets (complete confs): 414
using faster count positions algorithm for large data
unique positions, atoms: [138, 138, 95, 138, 59, 95, 19, 59, 19, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 138, 138, 138, 138, 414, 59, 59, 59, 19, 18, 19, 1, 19, 19] 414
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: 890
number of broken/clashed sets: 198
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071485 none C=CC(O)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
414  conformations in input
total number of sets (complete confs): 414
using faster count positions algorithm for large data
unique positions, atoms: [108, 64, 26, 64, 9, 26, 1, 9, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 108, 108, 108, 64, 192, 9, 9, 9, 1, 1, 1, 19, 1, 1] 414
rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 604
number of broken/clashed sets: 198
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071485 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071485
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071485/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071485
Building REAL250005071486
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071486'
/scratch/stefan/7916153/working/building/REAL250005071486 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071486

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071486/0 /scratch/stefan/7916153/working/building/REAL250005071486 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 617)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/617
`/scratch/stefan/7916153/working/3D/617' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C12CC1CC2)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071486.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071486.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071486/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071486 none CN(C(=O)C12CC1CC2)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 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]
dock color type numbers: [7, 7, 7, 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, 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: [6, 1, 6, 18, 18, 22, 22, 22, 22, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 19, 1, 1] 53
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 80
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071486 none CN(C(=O)C12CC1CC2)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 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]
dock color type numbers: [7, 7, 7, 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, 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: [10, 5, 1, 5, 1, 1, 1, 1, 1, 10, 22, 22, 22, 43, 43, 53, 53, 53, 53, 53, 22, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 53, 22, 22] 53
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36])
total number of confs: 154
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071486 none CN(C(=O)C12CC1CC2)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 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]
dock color type numbers: [7, 7, 7, 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, 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: [29, 19, 29, 48, 48, 53, 53, 53, 53, 19, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 29, 29, 29, 53, 53, 53, 53, 53, 53, 53, 19, 18, 19, 1, 19, 19] 53
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: 138
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071486 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071486
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071486/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071486
Building REAL250005071487
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071487'
/scratch/stefan/7916153/working/building/REAL250005071487 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071487

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071487/0 /scratch/stefan/7916153/working/building/REAL250005071487 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 618)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/618
`/scratch/stefan/7916153/working/3D/618' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C[C@H](C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071487.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071487.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071487/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071487 none C=C[C@H](C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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: [1, 1, 5, 7, 5, 5, 1, 11, 8, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [158, 158, 139, 158, 158, 65, 38, 65, 19, 38, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 158, 158, 158, 158, 158, 158, 139, 139, 38, 38, 38, 19, 19, 19, 1, 19, 19] 158
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: 587
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071487 none C=C[C@H](C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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: [1, 1, 5, 7, 5, 5, 1, 11, 8, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [111, 91, 67, 91, 91, 16, 6, 16, 1, 6, 1, 1, 1, 1, 6, 6, 18, 19, 19, 19, 19, 1, 111, 111, 111, 91, 91, 91, 67, 67, 6, 6, 6, 1, 1, 1, 19, 1, 1] 158
rigid atoms, others: [33, 34, 35, 37, 38, 8, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 476
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071487 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071487
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071487/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071487
Building REAL250005071488
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071488'
/scratch/stefan/7916153/working/building/REAL250005071488 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071488

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071488/0 /scratch/stefan/7916153/working/building/REAL250005071488 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 619)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/619
`/scratch/stefan/7916153/working/3D/619' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C=CC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071488.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071488.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071488/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071488 none CN(C(=O)C=CC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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, 7, 7]
0  hydrogens 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, 22, 22, 74, 74, 149, 149, 1, 1, 1, 1, 7, 7, 20, 21, 21, 21, 21, 1, 7, 7, 7, 74, 74, 149, 149, 149, 149, 149, 1, 1, 1, 21, 1, 1] 201
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 468
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071488 none CN(C(=O)C=CC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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, 7, 7]
0  hydrogens 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, 64, 10, 63, 10, 1, 1, 1, 1, 121, 149, 149, 149, 195, 195, 201, 201, 201, 201, 201, 149, 121, 121, 121, 10, 10, 1, 1, 1, 1, 1, 149, 149, 149, 201, 149, 149] 201
rigid atoms, others: [5, 6, 7, 8, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36])
total number of confs: 613
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071488 none CN(C(=O)C=CC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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, 7, 7]
0  hydrogens 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, 21, 55, 103, 103, 171, 171, 201, 201, 21, 21, 6, 1, 6, 1, 1, 1, 1, 1, 1, 21, 55, 55, 55, 171, 171, 201, 201, 201, 201, 201, 21, 21, 21, 1, 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])
total number of confs: 617
number of broken/clashed sets: 34
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071488 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071488
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071488/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071488
Building REAL250005071489
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071489'
/scratch/stefan/7916153/working/building/REAL250005071489 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071489

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071489/0 /scratch/stefan/7916153/working/building/REAL250005071489 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 620)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/620
`/scratch/stefan/7916153/working/3D/620' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C#N)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071489.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071489.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071489/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071489 none CCC(C#N)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [193, 183, 138, 183, 183, 84, 138, 27, 84, 27, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 27, 201, 201, 201, 201, 201, 183, 84, 84, 84, 27, 26, 26, 1, 27, 27] 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: 770
number of broken/clashed sets: 100
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071489 none CCC(C#N)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [85, 68, 31, 68, 68, 9, 31, 1, 9, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 93, 93, 93, 93, 93, 68, 9, 9, 9, 1, 1, 1, 27, 1, 1] 201
rigid atoms, others: [32, 34, 35, 7, 9, 10, 11, 12, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 492
number of broken/clashed sets: 100
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071489 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071489
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071489/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071489
Building REAL250005071490
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071490'
/scratch/stefan/7916153/working/building/REAL250005071490 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071490

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071490/0 /scratch/stefan/7916153/working/building/REAL250005071490 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 621)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/621
`/scratch/stefan/7916153/working/3D/621' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1C2CCC21)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071490.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071490.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071490/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071490 none CN(C(=O)C1C2CCC21)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 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]
dock color type numbers: [7, 7, 7, 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, 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, 22, 22, 44, 44, 44, 44, 1, 1, 1, 1, 4, 4, 22, 22, 22, 22, 22, 1, 7, 7, 7, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 23, 1, 1] 90
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 153
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071490 none CN(C(=O)C1C2CCC21)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 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]
dock color type numbers: [7, 7, 7, 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, 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: [26, 8, 1, 8, 1, 1, 1, 1, 1, 26, 44, 44, 44, 70, 70, 90, 90, 90, 90, 90, 44, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 90, 44, 44] 90
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36])
total number of confs: 259
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071490 none CN(C(=O)C1C2CCC21)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 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]
dock color type numbers: [7, 7, 7, 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, 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: [47, 23, 47, 66, 66, 90, 90, 90, 90, 23, 22, 11, 1, 11, 1, 1, 1, 1, 1, 1, 23, 47, 47, 47, 90, 90, 90, 90, 90, 90, 90, 23, 22, 23, 1, 23, 23] 90
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: 267
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071490 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071490
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071490/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071490
Building REAL250005071491
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071491'
/scratch/stefan/7916153/working/building/REAL250005071491 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071491

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071491/0 /scratch/stefan/7916153/working/building/REAL250005071491 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 622)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/622
`/scratch/stefan/7916153/working/3D/622' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CCC1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071491.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071491.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071491/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071491 none C=C1CCC1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 29, 29, 18, 7, 18, 1, 7, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 1, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 1, 1, 1, 17, 1, 1] 55
rigid atoms, others: [32, 33, 35, 36, 7, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 107
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071491 none C=C1CCC1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 6, 17, 17, 29, 29, 29, 48, 48, 55, 55, 55, 55, 55, 29, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 29, 29, 29, 55, 29, 29] 55
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: 169
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071491 none C=C1CCC1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 55, 44, 33, 44, 18, 33, 18, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 55, 55, 55, 55, 55, 55, 55, 33, 33, 33, 18, 17, 17, 1, 18, 18] 55
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: 160
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071491 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071491
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071491/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071491
Building REAL250005071492
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071492'
/scratch/stefan/7916153/working/building/REAL250005071492 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071492

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071492/0 /scratch/stefan/7916153/working/building/REAL250005071492 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 623)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/623
`/scratch/stefan/7916153/working/3D/623' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1C(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)[C@H]1C)

`REAL250005071492.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071492.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071492/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071492 none C[C@H]1C(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)[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', 'C.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, 7, 5, 1, 11, 8, 5, 5, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 52, 52, 19, 6, 19, 1, 6, 1, 1, 1, 1, 4, 4, 17, 17, 17, 17, 17, 1, 52, 52, 52, 52, 52, 52, 52, 7, 7, 7, 1, 1, 1, 17, 1, 1, 52, 52, 52] 96
rigid atoms, others: [32, 34, 35, 6, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 36, 37, 38])
total number of confs: 170
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071492 none C[C@H]1C(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)[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', 'C.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, 7, 5, 1, 11, 8, 5, 5, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 28, 28, 52, 52, 52, 79, 79, 96, 96, 96, 96, 96, 52, 1, 1, 1, 2, 2, 2, 1, 28, 28, 28, 52, 52, 52, 96, 52, 52, 2, 2, 2] 96
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: 298
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071492 none C[C@H]1C(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)[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', 'C.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, 7, 5, 1, 11, 8, 5, 5, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 61, 39, 61, 17, 39, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 96, 96, 96, 96, 96, 96, 96, 39, 39, 39, 17, 17, 17, 1, 17, 17, 96, 96, 96] 96
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: 293
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071492 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071492
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071492/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071492
Building REAL250005071493
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071493'
/scratch/stefan/7916153/working/building/REAL250005071493 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL250005071493

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071493/0 /scratch/stefan/7916153/working/building/REAL250005071493 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 624)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/624
`/scratch/stefan/7916153/working/3D/624' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@H+](C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071493.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071493.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071493/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071493 none CC[N@H+](C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 9, 6, 5, 5, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 12, 12, 10, 10, 10, 7, 10, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 10, 10, 10, 7, 7, 7, 1, 7, 7] 12
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: 37
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071493 none CC[N@H+](C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 9, 6, 5, 5, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 6, 10, 10, 5, 5, 5, 1, 5, 1, 1, 1, 1, 3, 3, 6, 7, 7, 7, 7, 1, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 5, 5, 5, 1, 1, 1, 7, 1, 1] 12
rigid atoms, others: [35, 36, 37, 39, 8, 10, 11, 12, 13, 40, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 53
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071493 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071493/1 /scratch/stefan/7916153/working/building/REAL250005071493 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 625)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/625
`/scratch/stefan/7916153/working/3D/625' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@@H+](C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071493.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071493.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071493/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071493 none CC[N@@H+](C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 9, 6, 5, 5, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 8, 8, 8, 5, 8, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 5, 5, 5, 1, 5, 5] 9
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: 27
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071493 none CC[N@@H+](C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 9, 6, 5, 5, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 5, 7, 7, 4, 4, 4, 1, 4, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 4, 4, 4, 1, 1, 1, 5, 1, 1] 9
rigid atoms, others: [35, 36, 37, 39, 8, 10, 11, 12, 13, 40, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38])
total number of confs: 36
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071493 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `2'
/scratch/stefan/7916153/working/building/REAL250005071493/2 /scratch/stefan/7916153/working/building/REAL250005071493 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 2 (index: 626)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/626
`/scratch/stefan/7916153/working/3D/626' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN(C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071493.mol2' -> `2.mol2'
`temp.mol2' -> `REAL250005071493.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071493/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071493 none CCN(C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 10, 5, 5, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 182, 197, 112, 58, 112, 15, 58, 15, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 201, 201, 201, 201, 201, 197, 197, 197, 182, 182, 58, 58, 58, 15, 14, 15, 1, 15, 15] 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: 694
number of broken/clashed sets: 86
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071493 none CCN(C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 10, 5, 5, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 119, 89, 119, 29, 9, 29, 1, 9, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 145, 145, 145, 145, 145, 119, 119, 119, 89, 89, 9, 9, 9, 1, 1, 1, 15, 1, 1] 201
rigid atoms, others: [34, 35, 36, 38, 7, 9, 10, 11, 12, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37])
total number of confs: 616
number of broken/clashed sets: 86
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071493 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071493
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
2: /scratch/stefan/7916153/working/building/REAL250005071493/2.*
1: /scratch/stefan/7916153/working/building/REAL250005071493/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071493/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071493
Building REAL250005071494
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071494'
/scratch/stefan/7916153/working/building/REAL250005071494 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071494

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071494/0 /scratch/stefan/7916153/working/building/REAL250005071494 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 627)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/627
`/scratch/stefan/7916153/working/3D/627' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071494.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071494.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071494/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071494 none CC(O)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
252  conformations in input
total number of sets (complete confs): 252
using faster count positions algorithm for large data
unique positions, atoms: [84, 77, 84, 56, 77, 22, 56, 22, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 84, 84, 84, 84, 252, 56, 56, 56, 22, 21, 22, 1, 22, 22] 252
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: 503
number of broken/clashed sets: 126
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071494 none CC(O)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
252  conformations in input
total number of sets (complete confs): 252
using faster count positions algorithm for large data
unique positions, atoms: [44, 23, 44, 9, 23, 1, 9, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 44, 44, 44, 44, 132, 9, 9, 9, 1, 1, 1, 22, 1, 1] 252
rigid atoms, others: [32, 5, 7, 8, 9, 10, 18, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 335
number of broken/clashed sets: 126
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071494 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071494
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071494/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071494
Building REAL250005071495
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071495'
/scratch/stefan/7916153/working/building/REAL250005071495 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071495

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071495/0 /scratch/stefan/7916153/working/building/REAL250005071495 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 628)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/628
`/scratch/stefan/7916153/working/3D/628' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071495.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071495.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071495/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071495 none CC(=O)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [146, 122, 146, 100, 122, 30, 100, 30, 29, 11, 1, 11, 1, 1, 1, 1, 1, 1, 30, 146, 146, 146, 100, 100, 100, 30, 29, 29, 1, 30, 30] 146
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])
total number of confs: 417
number of broken/clashed sets: 62
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071495 none CC(=O)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [63, 27, 63, 9, 27, 1, 9, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 1, 63, 63, 63, 9, 9, 9, 1, 1, 1, 29, 1, 1] 146
rigid atoms, others: [5, 7, 8, 9, 10, 18, 25, 26, 27, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 28])
total number of confs: 216
number of broken/clashed sets: 62
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071495 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071495
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071495/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071495
Building REAL250005071496
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071496'
/scratch/stefan/7916153/working/building/REAL250005071496 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071496

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071496/0 /scratch/stefan/7916153/working/building/REAL250005071496 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 629)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/629
`/scratch/stefan/7916153/working/3D/629' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CCCC#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071496.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071496.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071496/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071496 none CN(C(=O)CCCC#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 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, 7]
0  hydrogens 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, 9, 31, 49, 49, 115, 130, 201, 201, 9, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 31, 31, 31, 115, 115, 147, 147, 191, 191, 9, 8, 9, 1, 9, 9] 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: 920
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071496 none CN(C(=O)CCCC#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 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, 7]
0  hydrogens 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, 22, 22, 69, 80, 149, 149, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 1, 9, 9, 9, 69, 69, 97, 97, 137, 140, 1, 1, 1, 9, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 9, 10, 11, 12, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 724
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071496 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071496
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071496/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071496
Building REAL250005071497
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071497'
/scratch/stefan/7916153/working/building/REAL250005071497 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071497

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071497/0 /scratch/stefan/7916153/working/building/REAL250005071497 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 630)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/630
`/scratch/stefan/7916153/working/3D/630' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1(C#N)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071497.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071497.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071497/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071497 none CN(C(=O)C1(C#N)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 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]
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: [9, 1, 9, 21, 21, 25, 25, 25, 25, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 9, 9, 9, 25, 25, 25, 25, 1, 1, 1, 18, 1, 1] 55
rigid atoms, others: [32, 1, 33, 9, 10, 11, 12, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 93
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071497 none CN(C(=O)C1(C#N)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 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]
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: [10, 4, 1, 4, 1, 1, 1, 1, 1, 10, 25, 25, 25, 45, 45, 55, 55, 55, 55, 55, 25, 10, 10, 10, 1, 1, 1, 1, 25, 25, 25, 55, 25, 25] 55
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33])
total number of confs: 161
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071497 none CN(C(=O)C1(C#N)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 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]
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: [39, 18, 39, 53, 53, 55, 55, 55, 55, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 39, 39, 39, 55, 55, 55, 55, 18, 18, 18, 1, 18, 18] 55
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])
total number of confs: 146
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071497 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071497
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071497/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071497
Building REAL250005071498
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071498'
/scratch/stefan/7916153/working/building/REAL250005071498 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071498

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071498/0 /scratch/stefan/7916153/working/building/REAL250005071498 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 631)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/631
`/scratch/stefan/7916153/working/3D/631' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)C1)

`REAL250005071498.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071498.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071498/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071498 none C=C1CC(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [47, 47, 47, 20, 7, 20, 1, 7, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 47, 47, 47, 47, 47, 47, 7, 7, 7, 1, 1, 1, 21, 1, 1, 47, 47] 88
rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 35, 36])
total number of confs: 163
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071498 none C=C1CC(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 23, 23, 47, 47, 47, 71, 71, 88, 88, 88, 88, 88, 47, 1, 1, 1, 1, 1, 1, 23, 23, 23, 47, 47, 47, 88, 47, 47, 1, 1] 88
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: 255
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071498 none C=C1CC(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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
88  conformations in input
total number of sets (complete confs): 88
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 67, 45, 67, 21, 45, 21, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 88, 88, 88, 88, 88, 88, 45, 45, 45, 21, 20, 21, 1, 21, 21, 88, 88] 88
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: 269
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071498 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071498
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071498/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071498
Building REAL250005071499
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071499'
/scratch/stefan/7916153/working/building/REAL250005071499 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071499

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071499/0 /scratch/stefan/7916153/working/building/REAL250005071499 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 632)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/632
`/scratch/stefan/7916153/working/3D/632' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1(F)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071499.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071499.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071499/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071499 none CN(C(=O)C1(F)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 5, 15, 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]
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]
0  hydrogens need rotated
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 20, 20, 43, 43, 43, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 1, 8, 8, 8, 43, 43, 43, 43, 1, 1, 1, 17, 1, 1] 67
rigid atoms, others: [32, 1, 8, 9, 10, 11, 19, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 143
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071499 none CN(C(=O)C1(F)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 5, 15, 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]
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]
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: [28, 8, 1, 8, 1, 1, 1, 1, 28, 43, 43, 43, 61, 61, 67, 67, 67, 67, 67, 43, 28, 28, 28, 1, 1, 1, 1, 43, 43, 43, 67, 43, 43] 67
rigid atoms, others: [2, 4, 5, 6, 7, 23, 24, 25, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32])
total number of confs: 203
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071499 none CN(C(=O)C1(F)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 5, 15, 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]
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]
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: [37, 17, 37, 50, 50, 67, 67, 67, 17, 17, 10, 1, 10, 1, 1, 1, 1, 1, 1, 17, 37, 37, 37, 67, 67, 67, 67, 17, 17, 17, 1, 17, 17] 67
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: 203
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071499 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071499
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071499/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071499
Building REAL250005071500
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071500'
/scratch/stefan/7916153/working/building/REAL250005071500 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071500

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071500/0 /scratch/stefan/7916153/working/building/REAL250005071500 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 633)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/633
`/scratch/stefan/7916153/working/3D/633' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071500.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071500.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071500/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071500 none COC(C)(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [110, 110, 88, 110, 110, 65, 88, 23, 65, 23, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 110, 110, 110, 110, 110, 110, 110, 110, 110, 65, 65, 65, 23, 22, 22, 1, 23, 23] 110
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: 352
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071500 none COC(C)(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [52, 34, 21, 34, 34, 9, 21, 1, 9, 1, 1, 1, 1, 6, 6, 22, 22, 22, 23, 23, 1, 52, 52, 52, 34, 34, 34, 34, 34, 34, 9, 9, 9, 1, 1, 1, 23, 1, 1] 110
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 205
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071500 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071500
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071500/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071500
Building REAL250005071501
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071501'
/scratch/stefan/7916153/working/building/REAL250005071501 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071501

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071501/0 /scratch/stefan/7916153/working/building/REAL250005071501 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 634)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/634
`/scratch/stefan/7916153/working/3D/634' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC#N)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071501.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071501.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071501/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071501 none CC(CC#N)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [83, 58, 83, 106, 106, 37, 58, 10, 37, 10, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 83, 83, 83, 83, 106, 106, 37, 37, 37, 10, 9, 9, 1, 10, 9] 106
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: 426
number of broken/clashed sets: 56
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071501 none CC(CC#N)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [45, 24, 45, 70, 70, 9, 24, 1, 9, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 1, 45, 45, 45, 45, 70, 70, 9, 9, 9, 1, 1, 1, 9, 1, 1] 106
rigid atoms, others: [32, 34, 35, 7, 9, 10, 11, 12, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 307
number of broken/clashed sets: 56
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071501 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071501
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071501/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071501
Building REAL250005071502
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071502'
/scratch/stefan/7916153/working/building/REAL250005071502 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071502

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071502/0 /scratch/stefan/7916153/working/building/REAL250005071502 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 635)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/635
`/scratch/stefan/7916153/working/3D/635' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1CC1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071502.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071502.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071502/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071502 none CCC1CC1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 36, 36, 20, 7, 20, 1, 7, 1, 1, 1, 1, 4, 4, 19, 20, 20, 20, 20, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 7, 7, 7, 1, 1, 1, 20, 1, 1] 75
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 136
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071502 none CCC1CC1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 7, 7, 19, 19, 36, 36, 36, 60, 60, 75, 75, 75, 75, 75, 36, 2, 2, 2, 2, 2, 1, 1, 1, 1, 19, 19, 19, 36, 36, 36, 75, 36, 36] 75
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: 231
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071502 none CCC1CC1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 61, 43, 61, 20, 43, 20, 20, 11, 1, 11, 1, 1, 1, 1, 1, 1, 20, 75, 75, 75, 75, 75, 75, 75, 75, 75, 43, 43, 43, 20, 20, 20, 1, 20, 20] 75
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: 208
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071502 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071502
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071502/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071502
Building REAL250005071503
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071503'
/scratch/stefan/7916153/working/building/REAL250005071503 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071503

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071503/0 /scratch/stefan/7916153/working/building/REAL250005071503 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 636)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/636
`/scratch/stefan/7916153/working/3D/636' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(C)(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071503.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071503.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071503/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071503 none C=CC(C)(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
261  conformations in input
total number of sets (complete confs): 261
using faster count positions algorithm for large data
unique positions, atoms: [87, 87, 69, 87, 87, 43, 69, 19, 43, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 87, 87, 87, 87, 87, 87, 261, 43, 43, 43, 19, 18, 18, 1, 18, 18] 261
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: 545
number of broken/clashed sets: 142
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071503 none C=CC(C)(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
261  conformations in input
total number of sets (complete confs): 261
using faster count positions algorithm for large data
unique positions, atoms: [61, 41, 25, 41, 41, 9, 25, 1, 9, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 61, 61, 61, 41, 41, 41, 123, 9, 9, 9, 1, 1, 1, 18, 1, 1] 261
rigid atoms, others: [32, 33, 35, 36, 7, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 368
number of broken/clashed sets: 142
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071503 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071503
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071503/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071503
Building REAL250005071504
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071504'
/scratch/stefan/7916153/working/building/REAL250005071504 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071504

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071504/0 /scratch/stefan/7916153/working/building/REAL250005071504 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 637)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/637
`/scratch/stefan/7916153/working/3D/637' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071504.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071504.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071504/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071504 none CCCC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 128, 128, 60, 35, 60, 13, 35, 13, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 181, 181, 128, 128, 35, 35, 35, 13, 12, 13, 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: 791
number of broken/clashed sets: 62
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071504 none CCCC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [174, 139, 83, 83, 22, 9, 22, 1, 9, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 1, 174, 174, 174, 174, 174, 139, 139, 83, 83, 9, 9, 9, 1, 1, 1, 13, 1, 1] 201
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 745
number of broken/clashed sets: 62
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071504 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071504
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071504/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071504
Building REAL250005071505
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071505'
/scratch/stefan/7916153/working/building/REAL250005071505 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071505

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071505/0 /scratch/stefan/7916153/working/building/REAL250005071505 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 638)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/638
`/scratch/stefan/7916153/working/3D/638' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(F)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071505.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071505.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071505/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071505 none CC=C(F)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [153, 153, 126, 153, 84, 126, 25, 84, 25, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 153, 153, 153, 153, 84, 84, 84, 25, 24, 24, 1, 24, 24] 153
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: 442
number of broken/clashed sets: 65
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071505 none CC=C(F)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 31, 78, 9, 31, 1, 9, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 78, 78, 78, 78, 9, 9, 9, 1, 1, 1, 24, 1, 1] 153
rigid atoms, others: [32, 6, 8, 9, 10, 11, 19, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 252
number of broken/clashed sets: 65
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071505 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071505
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071505/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071505
Building REAL250005071506
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071506'
/scratch/stefan/7916153/working/building/REAL250005071506 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071506

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071506/0 /scratch/stefan/7916153/working/building/REAL250005071506 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 639)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/639
`/scratch/stefan/7916153/working/3D/639' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C)

`REAL250005071506.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071506.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071506/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071506 none C[C@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 7, 3, 7, 3, 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
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 5, 2, 5, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 2, 2, 1, 2, 2, 5, 5, 5, 5, 5, 5] 5
rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 15
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071506 none C[C@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 7, 3, 7, 3, 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
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 1, 1, 4, 4, 4, 4, 4, 4] 5
rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 13
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071506 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071506/1 /scratch/stefan/7916153/working/building/REAL250005071506 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 640)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/640
`/scratch/stefan/7916153/working/3D/640' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C)

`REAL250005071506.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071506.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071506/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071506 none C[C@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [97, 78, 97, 50, 78, 16, 50, 16, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 97, 100, 100, 97, 97, 97, 50, 50, 50, 16, 15, 15, 1, 16, 16, 100, 100, 100, 100, 100, 100] 100
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, 39])
total number of confs: 327
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071506 none C[C@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [53, 27, 53, 9, 27, 1, 9, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 53, 64, 64, 53, 53, 53, 9, 9, 9, 1, 1, 1, 15, 1, 1, 64, 64, 64, 64, 64, 64] 100
rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 253
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071506 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071506
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071506/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071506/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071506
Building REAL250005071507
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071507'
/scratch/stefan/7916153/working/building/REAL250005071507 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071507

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071507/0 /scratch/stefan/7916153/working/building/REAL250005071507 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 641)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/641
`/scratch/stefan/7916153/working/3D/641' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071507.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071507.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071507/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071507 none CCOC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 11, 8, 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]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 194, 146, 146, 70, 40, 70, 16, 40, 16, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 201, 201, 201, 201, 201, 146, 146, 40, 40, 40, 16, 15, 16, 1, 16, 16] 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: 530
number of broken/clashed sets: 72
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071507 none CCOC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 11, 8, 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]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [171, 156, 88, 88, 26, 9, 26, 1, 9, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 171, 171, 171, 171, 171, 88, 88, 9, 9, 9, 1, 1, 1, 16, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 7, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 455
number of broken/clashed sets: 72
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071507 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071507
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071507/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071507
Building REAL250005071508
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071508'
/scratch/stefan/7916153/working/building/REAL250005071508 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071508

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071508/0 /scratch/stefan/7916153/working/building/REAL250005071508 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 642)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/642
`/scratch/stefan/7916153/working/3D/642' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)OCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071508.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071508.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071508/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071508 none CC(=O)OCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 12, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 151, 58, 39, 58, 11, 39, 11, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 201, 201, 201, 151, 151, 39, 39, 39, 11, 10, 11, 1, 11, 11] 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: 633
number of broken/clashed sets: 96
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071508 none CC(=O)OCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 12, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 145, 146, 70, 19, 9, 19, 1, 9, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 1, 146, 146, 146, 70, 70, 9, 9, 9, 1, 1, 1, 11, 1, 1] 201
rigid atoms, others: [33, 34, 7, 9, 10, 11, 12, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 379
number of broken/clashed sets: 96
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071508 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071508
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071508/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071508
Building REAL250005071509
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071509'
/scratch/stefan/7916153/working/building/REAL250005071509 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071509

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071509/0 /scratch/stefan/7916153/working/building/REAL250005071509 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 643)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/643
`/scratch/stefan/7916153/working/3D/643' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071509.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071509.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071509/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071509 none CC(=O)C=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 1, 1, 11, 8, 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]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 124, 130, 124, 88, 57, 88, 19, 57, 19, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 130, 130, 130, 124, 124, 57, 57, 57, 19, 18, 19, 1, 19, 19] 130
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: 378
number of broken/clashed sets: 59
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071509 none CC(=O)C=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 1, 1, 11, 8, 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]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [99, 71, 99, 71, 29, 9, 29, 1, 9, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 99, 99, 99, 71, 71, 9, 9, 9, 1, 1, 1, 19, 1, 1] 130
rigid atoms, others: [33, 34, 7, 9, 10, 11, 12, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 317
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071509 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071509
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071509/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071509
Building REAL250005071510
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071510'
/scratch/stefan/7916153/working/building/REAL250005071510 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071510

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071510/0 /scratch/stefan/7916153/working/building/REAL250005071510 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 644)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/644
`/scratch/stefan/7916153/working/3D/644' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)COC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071510.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071510.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071510/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071510 none CN(C(=O)COC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 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, 7]
0  hydrogens 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, 17, 17, 41, 88, 142, 142, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 1, 9, 9, 9, 41, 41, 142, 142, 142, 142, 142, 1, 1, 1, 14, 1, 1] 201
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 424
number of broken/clashed sets: 73
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071510 none CN(C(=O)COC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [97, 62, 26, 62, 6, 1, 1, 1, 1, 97, 142, 142, 142, 201, 201, 201, 201, 201, 201, 201, 142, 97, 97, 97, 26, 26, 1, 1, 1, 1, 1, 142, 142, 142, 201, 142, 142] 201
rigid atoms, others: [5, 6, 7, 8, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36])
total number of confs: 658
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071510 none CN(C(=O)COC1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 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, 7]
0  hydrogens 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, 14, 45, 72, 72, 125, 170, 201, 201, 14, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 45, 45, 45, 125, 125, 201, 201, 201, 201, 201, 14, 13, 14, 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: 666
number of broken/clashed sets: 73
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071510 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071510
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071510/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071510
Building REAL250005071511
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071511'
/scratch/stefan/7916153/working/building/REAL250005071511 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071511

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071511/0 /scratch/stefan/7916153/working/building/REAL250005071511 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 645)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/645
`/scratch/stefan/7916153/working/3D/645' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=NC=CN1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071511.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071511.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071511/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071511 none CN(C(=O)C1=NC=CN1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 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]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 7, 15, 15, 22, 22, 22, 22, 1, 1, 1, 1, 5, 5, 20, 20, 20, 20, 20, 1, 7, 7, 7, 22, 22, 22, 1, 1, 1, 21, 1, 1] 42
rigid atoms, others: [32, 1, 9, 10, 11, 12, 20, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 82
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071511 none CN(C(=O)C1=NC=CN1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 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]
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: [16, 6, 1, 6, 1, 1, 1, 1, 1, 16, 31, 31, 31, 45, 45, 53, 53, 53, 53, 53, 31, 16, 16, 16, 1, 1, 1, 31, 31, 31, 53, 31, 31] 53
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32])
total number of confs: 149
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071511 none CN(C(=O)C1=NC=CN1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 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]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [34, 21, 34, 42, 42, 42, 42, 42, 42, 21, 20, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 34, 34, 34, 42, 42, 42, 21, 20, 21, 1, 21, 21] 42
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: 109
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071511 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071511
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071511/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071511
Building REAL250005071512
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071512'
/scratch/stefan/7916153/working/building/REAL250005071512 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071512

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071512/0 /scratch/stefan/7916153/working/building/REAL250005071512 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 646)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/646
`/scratch/stefan/7916153/working/3D/646' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CO)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071512.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071512.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071512/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071512 none CC(CO)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 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
501  conformations in input
total number of sets (complete confs): 501
using faster count positions algorithm for large data
unique positions, atoms: [163, 129, 163, 167, 81, 129, 25, 81, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 163, 163, 163, 163, 167, 167, 501, 81, 81, 81, 25, 24, 24, 1, 25, 24] 501
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: 1056
number of broken/clashed sets: 257
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071512 none CC(CO)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 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
501  conformations in input
total number of sets (complete confs): 501
using faster count positions algorithm for large data
unique positions, atoms: [68, 32, 68, 117, 9, 32, 1, 9, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 68, 68, 68, 68, 117, 117, 351, 9, 9, 9, 1, 1, 1, 24, 1, 1] 501
rigid atoms, others: [32, 34, 35, 6, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 881
number of broken/clashed sets: 257
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071512 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071512
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071512/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071512
Building REAL250005071513
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071513'
/scratch/stefan/7916153/working/building/REAL250005071513 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071513

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071513/0 /scratch/stefan/7916153/working/building/REAL250005071513 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 647)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/647
`/scratch/stefan/7916153/working/3D/647' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CON=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071513.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071513.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071513/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071513 none CN(C(=O)C1=CON=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 1, 12, 8, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 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
198  conformations in input
total number of sets (complete confs): 198
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 31, 31, 100, 100, 100, 100, 1, 1, 1, 1, 6, 6, 23, 23, 24, 23, 23, 1, 9, 9, 9, 100, 100, 1, 1, 1, 23, 1, 1] 198
rigid atoms, others: [1, 9, 10, 11, 12, 20, 26, 27, 28, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29])
total number of confs: 210
number of broken/clashed sets: 83
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071513 none CN(C(=O)C1=CON=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 1, 12, 8, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 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
198  conformations in input
total number of sets (complete confs): 198
using faster count positions algorithm for large data
unique positions, atoms: [37, 11, 1, 11, 1, 1, 1, 1, 1, 37, 100, 100, 100, 178, 178, 198, 198, 198, 198, 198, 100, 37, 37, 37, 1, 1, 100, 100, 100, 198, 100, 100] 198
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 559
number of broken/clashed sets: 83
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071513 none CN(C(=O)C1=CON=C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 1, 12, 8, 1, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 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
198  conformations in input
total number of sets (complete confs): 198
using faster count positions algorithm for large data
unique positions, atoms: [83, 24, 83, 128, 128, 198, 198, 198, 198, 24, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 83, 83, 83, 198, 198, 24, 23, 23, 1, 23, 23] 198
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 479
number of broken/clashed sets: 83
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071513 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071513
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071513/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071513
Building REAL250005071514
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071514'
/scratch/stefan/7916153/working/building/REAL250005071514 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071514

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071514/0 /scratch/stefan/7916153/working/building/REAL250005071514 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 648)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/648
`/scratch/stefan/7916153/working/3D/648' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CCCCO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071514.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071514.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071514/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071514 none CN(C(=O)CCCCO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 12, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 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, 7, 7, 7, 7]
1  hydrogens 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, 11, 29, 53, 53, 141, 165, 200, 200, 11, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 141, 141, 174, 174, 200, 200, 201, 201, 600, 11, 10, 11, 1, 11, 11] 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: 1489
number of broken/clashed sets: 207
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071514 none CN(C(=O)CCCCO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 12, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 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, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 22, 22, 79, 101, 127, 161, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 1, 9, 9, 9, 79, 79, 108, 108, 127, 127, 162, 162, 483, 1, 1, 1, 11, 1, 1] 603
rigid atoms, others: [1, 34, 35, 37, 38, 33, 9, 10, 11, 12, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 1276
number of broken/clashed sets: 207
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071514 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071514
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071514/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071514
Building REAL250005071515
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071515'
/scratch/stefan/7916153/working/building/REAL250005071515 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071515

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071515/0 /scratch/stefan/7916153/working/building/REAL250005071515 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 649)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/649
`/scratch/stefan/7916153/working/3D/649' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C(=O)C1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071515.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071515.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071515/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071515 none CN(C(=O)C(=O)C1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 11, 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]
dock color type numbers: [7, 7, 7, 6, 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]
0  hydrogens 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, 24, 24, 57, 57, 151, 151, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 1, 9, 9, 9, 151, 151, 151, 151, 151, 1, 1, 1, 13, 1, 1] 201
rigid atoms, others: [1, 34, 33, 9, 10, 11, 12, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 440
number of broken/clashed sets: 85
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071515 none CN(C(=O)C(=O)C1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 11, 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]
dock color type numbers: [7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [83, 38, 12, 38, 1, 12, 1, 1, 1, 83, 151, 151, 151, 201, 201, 201, 201, 201, 201, 201, 151, 83, 83, 83, 1, 1, 1, 1, 1, 151, 151, 151, 201, 151, 151] 201
rigid atoms, others: [4, 6, 7, 8, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34])
total number of confs: 627
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071515 none CN(C(=O)C(=O)C1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 11, 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]
dock color type numbers: [7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 14, 63, 99, 99, 130, 130, 201, 201, 14, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 63, 63, 63, 201, 201, 201, 201, 201, 14, 13, 13, 1, 14, 14] 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: 609
number of broken/clashed sets: 85
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071515 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071515
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071515/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071515
Building REAL250005071516
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071516'
/scratch/stefan/7916153/working/building/REAL250005071516 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071516

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071516/0 /scratch/stefan/7916153/working/building/REAL250005071516 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 650)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/650
`/scratch/stefan/7916153/working/3D/650' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CC1(O)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071516.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071516.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071516/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071516 none CN(C(=O)CC1(O)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 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]
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: [7, 1, 7, 23, 23, 76, 122, 122, 122, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 17, 1, 8, 8, 8, 76, 76, 366, 122, 122, 122, 122, 1, 1, 1, 17, 1, 1] 549
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 823
number of broken/clashed sets: 152
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071516 none CN(C(=O)CC1(O)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 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]
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: [68, 31, 8, 31, 1, 1, 1, 1, 1, 68, 122, 122, 122, 176, 176, 183, 183, 183, 183, 183, 122, 68, 68, 68, 8, 8, 6, 1, 1, 1, 1, 122, 122, 122, 183, 122, 122] 549
rigid atoms, others: [4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36])
total number of confs: 599
number of broken/clashed sets: 152
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071516 none CN(C(=O)CC1(O)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 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]
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: [47, 17, 47, 87, 87, 147, 183, 183, 183, 17, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 47, 47, 47, 147, 147, 549, 183, 183, 183, 183, 17, 17, 17, 1, 17, 17] 549
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: 1182
number of broken/clashed sets: 152
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071516 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071516
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071516/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071516
Building REAL250005071517
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071517'
/scratch/stefan/7916153/working/building/REAL250005071517 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071517

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071517/0 /scratch/stefan/7916153/working/building/REAL250005071517 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 651)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/651
`/scratch/stefan/7916153/working/3D/651' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1CCC1F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071517.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071517.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071517/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071517 none CN(C(=O)C1CCC1F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', '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, 5, 5, 5, 15, 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]
dock color type numbers: [7, 7, 7, 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, 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: [8, 1, 8, 17, 17, 29, 29, 29, 29, 1, 1, 1, 1, 4, 4, 16, 16, 16, 16, 16, 1, 9, 9, 9, 29, 29, 29, 29, 29, 29, 1, 1, 1, 16, 1, 1] 55
rigid atoms, others: [32, 1, 34, 35, 9, 10, 11, 12, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 111
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071517 none CN(C(=O)C1CCC1F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', '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, 5, 5, 5, 15, 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]
dock color type numbers: [7, 7, 7, 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, 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: [16, 6, 1, 6, 1, 1, 1, 1, 1, 16, 29, 29, 29, 46, 46, 55, 55, 55, 55, 55, 29, 16, 16, 16, 1, 1, 1, 1, 1, 1, 29, 29, 29, 55, 29, 29] 55
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35])
total number of confs: 163
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071517 none CN(C(=O)C1CCC1F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', '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, 5, 5, 5, 15, 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]
dock color type numbers: [7, 7, 7, 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, 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: [31, 17, 31, 44, 44, 55, 55, 55, 55, 17, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 31, 31, 31, 55, 55, 55, 55, 55, 55, 17, 17, 17, 1, 16, 16] 55
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: 162
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071517 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071517
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071517/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071517
Building REAL250005071518
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071518'
/scratch/stefan/7916153/working/building/REAL250005071518 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071518

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071518/0 /scratch/stefan/7916153/working/building/REAL250005071518 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 652)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/652
`/scratch/stefan/7916153/working/3D/652' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)[C@@H]1C[C@H]1CF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071518.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071518.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071518/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071518 none CN(C(=O)[C@@H]1C[C@H]1CF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 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]
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]
0  hydrogens 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, 28, 28, 87, 87, 87, 87, 87, 159, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 9, 9, 9, 87, 87, 159, 159, 1, 1, 1, 16, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 11, 12, 13, 14, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 598
number of broken/clashed sets: 75
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071518 none CN(C(=O)[C@@H]1C[C@H]1CF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 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]
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]
0  hydrogens 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, 8, 1, 8, 1, 1, 1, 1, 1, 1, 9, 34, 87, 87, 87, 152, 152, 181, 181, 181, 181, 181, 87, 34, 34, 34, 1, 1, 9, 9, 87, 87, 87, 181, 87, 87] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 26, 27] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 524
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071518 none CN(C(=O)[C@@H]1C[C@H]1CF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 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]
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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 16, 56, 97, 97, 181, 181, 181, 181, 181, 201, 16, 16, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 56, 56, 56, 181, 181, 201, 201, 16, 16, 16, 1, 16, 16] 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: 645
number of broken/clashed sets: 75
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071518 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071518
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071518/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071518
Building REAL250005071519
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071519'
/scratch/stefan/7916153/working/building/REAL250005071519 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071519

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071519/0 /scratch/stefan/7916153/working/building/REAL250005071519 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 653)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/653
`/scratch/stefan/7916153/working/3D/653' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CO)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071519.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071519.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071519/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071519 none CCC(CO)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [184, 169, 122, 169, 197, 68, 122, 21, 68, 21, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 197, 197, 197, 197, 197, 169, 197, 197, 591, 68, 68, 68, 21, 20, 21, 1, 21, 21] 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: 1571
number of broken/clashed sets: 353
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071519 none CCC(CO)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [82, 60, 31, 60, 128, 9, 31, 1, 9, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 92, 92, 92, 92, 92, 60, 128, 128, 384, 9, 9, 9, 1, 1, 1, 21, 1, 1] 603
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 1198
number of broken/clashed sets: 353
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071519 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071519
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071519/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071519
Building REAL250005071520
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071520'
/scratch/stefan/7916153/working/building/REAL250005071520 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071520

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071520/0 /scratch/stefan/7916153/working/building/REAL250005071520 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 654)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/654
`/scratch/stefan/7916153/working/3D/654' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)[C@@H]1C[C@@H]1C#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071520.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071520.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071520/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071520 none CN(C(=O)[C@@H]1C[C@@H]1C#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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]
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, 1, 6, 18, 18, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 2, 2, 8, 8, 8, 8, 8, 1, 7, 7, 7, 34, 34, 1, 1, 1, 9, 1, 1] 47
rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 22, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31])
total number of confs: 119
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071520 none CN(C(=O)[C@@H]1C[C@@H]1C#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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]
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: [18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 18, 34, 34, 34, 46, 46, 47, 47, 47, 47, 47, 34, 18, 18, 18, 1, 1, 34, 34, 34, 47, 34, 34] 47
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 26, 27] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 151
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071520 none CN(C(=O)[C@@H]1C[C@@H]1C#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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]
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: [22, 9, 22, 37, 37, 47, 47, 47, 47, 47, 47, 9, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 22, 22, 22, 47, 47, 9, 9, 9, 1, 8, 8] 47
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: 137
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071520 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071520
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071520/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071520
Building REAL250005071521
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071521'
/scratch/stefan/7916153/working/building/REAL250005071521 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071521

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071521/0 /scratch/stefan/7916153/working/building/REAL250005071521 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 655)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/655
`/scratch/stefan/7916153/working/3D/655' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=COCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071521.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071521.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071521/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071521 none CN(C(=O)C1=COCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 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
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 31, 31, 68, 68, 68, 68, 1, 1, 1, 1, 6, 6, 23, 24, 24, 23, 23, 1, 9, 9, 9, 68, 68, 68, 68, 68, 1, 1, 1, 24, 1, 1] 141
rigid atoms, others: [1, 34, 33, 9, 10, 11, 12, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 169
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071521 none CN(C(=O)C1=COCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 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
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [25, 8, 1, 8, 1, 1, 1, 1, 1, 25, 68, 68, 68, 125, 125, 141, 141, 141, 141, 141, 68, 25, 25, 25, 1, 1, 1, 1, 1, 68, 68, 68, 141, 68, 68] 141
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34])
total number of confs: 403
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071521 none CN(C(=O)C1=COCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 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
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [80, 24, 80, 115, 115, 141, 141, 141, 141, 24, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 80, 80, 80, 141, 141, 141, 141, 141, 24, 23, 24, 1, 24, 23] 141
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: 358
number of broken/clashed sets: 60
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071521 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071521
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071521/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071521
Building REAL250005071522
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071522'
/scratch/stefan/7916153/working/building/REAL250005071522 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071522

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071522/0 /scratch/stefan/7916153/working/building/REAL250005071522 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 656)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/656
`/scratch/stefan/7916153/working/3D/656' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1(O)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071522.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071522.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071522/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071522 none CN(C(=O)C1(O)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 12, 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]
dock color type numbers: [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]
1  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: [9, 1, 9, 16, 16, 26, 26, 26, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 9, 9, 9, 78, 26, 26, 26, 26, 1, 1, 1, 17, 1, 1] 174
rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 19, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 180
number of broken/clashed sets: 64
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071522 none CN(C(=O)C1(O)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 12, 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]
dock color type numbers: [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]
1  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: [15, 6, 1, 6, 1, 1, 1, 1, 15, 26, 26, 26, 47, 47, 58, 58, 58, 58, 58, 26, 15, 15, 15, 6, 1, 1, 1, 1, 26, 26, 26, 58, 26, 26] 174
rigid atoms, others: [2, 4, 5, 6, 7, 24, 25, 26, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33])
total number of confs: 178
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071522 none CN(C(=O)C1(O)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 12, 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]
dock color type numbers: [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]
1  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: [35, 17, 35, 44, 44, 58, 58, 58, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 35, 35, 35, 174, 58, 58, 58, 58, 17, 17, 17, 1, 17, 17] 174
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: 344
number of broken/clashed sets: 64
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071522 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071522
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071522/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071522
Building REAL250005071523
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071523'
/scratch/stefan/7916153/working/building/REAL250005071523 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071523

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071523/0 /scratch/stefan/7916153/working/building/REAL250005071523 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 657)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/657
`/scratch/stefan/7916153/working/3D/657' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071523.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071523.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071523/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071523 none CN(C(=O)C1=CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 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]
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]
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: [9, 1, 9, 29, 29, 56, 56, 56, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 9, 9, 9, 56, 56, 56, 56, 56, 1, 1, 1, 26, 1, 1] 114
rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 19, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 154
number of broken/clashed sets: 45
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071523 none CN(C(=O)C1=CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 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]
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]
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: [24, 11, 1, 11, 1, 1, 1, 1, 24, 56, 56, 56, 104, 104, 114, 114, 114, 114, 114, 56, 25, 25, 25, 1, 1, 1, 1, 1, 56, 56, 56, 114, 56, 56] 114
rigid atoms, others: [2, 4, 5, 6, 7, 23, 24, 25, 26, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33])
total number of confs: 335
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071523 none CN(C(=O)C1=CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 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]
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]
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: [80, 26, 80, 114, 114, 114, 114, 114, 26, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 80, 80, 80, 114, 114, 114, 114, 114, 26, 25, 26, 1, 26, 26] 114
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: 306
number of broken/clashed sets: 45
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071523 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071523
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071523/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071523
Building REAL250005071524
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071524'
/scratch/stefan/7916153/working/building/REAL250005071524 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071524

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071524/0 /scratch/stefan/7916153/working/building/REAL250005071524 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 658)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/658
`/scratch/stefan/7916153/working/3D/658' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CF)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071524.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071524.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071524/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071524 none CC(CF)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [136, 101, 136, 140, 61, 101, 16, 61, 16, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 136, 136, 136, 136, 140, 140, 61, 61, 61, 16, 15, 15, 1, 16, 15] 140
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: 492
number of broken/clashed sets: 70
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071524 none CC(CF)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [53, 28, 53, 105, 9, 28, 1, 9, 1, 1, 1, 1, 6, 6, 15, 15, 16, 15, 15, 1, 53, 53, 53, 53, 105, 105, 9, 9, 9, 1, 1, 1, 16, 1, 1] 140
rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 466
number of broken/clashed sets: 70
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071524 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071524
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071524/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071524
Building REAL250005071525
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071525'
/scratch/stefan/7916153/working/building/REAL250005071525 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071525

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071525/0 /scratch/stefan/7916153/working/building/REAL250005071525 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 659)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/659
`/scratch/stefan/7916153/working/3D/659' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(Cl)=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071525.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071525.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071525/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071525 none CC(Cl)=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 16, 1, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 142, 109, 72, 109, 24, 72, 24, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 142, 142, 142, 142, 72, 72, 72, 24, 23, 24, 1, 24, 24] 142
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: 428
number of broken/clashed sets: 59
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071525 none CC(Cl)=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 16, 1, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [68, 68, 68, 29, 9, 29, 1, 9, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 68, 68, 68, 68, 9, 9, 9, 1, 1, 1, 24, 1, 1] 142
rigid atoms, others: [32, 6, 8, 9, 10, 11, 19, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 219
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071525 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071525
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071525/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071525
Building REAL250005071526
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071526'
/scratch/stefan/7916153/working/building/REAL250005071526 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071526

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071526/0 /scratch/stefan/7916153/working/building/REAL250005071526 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 660)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/660
`/scratch/stefan/7916153/working/3D/660' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071526.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071526.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071526/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071526 none CC=CC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 93, 69, 93, 24, 69, 24, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 104, 104, 104, 104, 104, 69, 69, 69, 24, 23, 24, 1, 24, 24] 104
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: 297
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071526 none CC=CC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [67, 67, 27, 9, 27, 1, 9, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 67, 67, 67, 67, 67, 9, 9, 9, 1, 1, 1, 24, 1, 1] 104
rigid atoms, others: [32, 5, 7, 8, 9, 10, 18, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 222
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071526 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071526
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071526/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071526
Building REAL250005071527
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071527'
/scratch/stefan/7916153/working/building/REAL250005071527 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071527

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071527/0 /scratch/stefan/7916153/working/building/REAL250005071527 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 661)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/661
`/scratch/stefan/7916153/working/3D/661' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1(C)CC1F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071527.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071527.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071527/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071527 none CN(C(=O)C1(C)CC1F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', '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, 5, 5, 5, 15, 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]
dock color type numbers: [7, 7, 7, 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, 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, 1, 9, 18, 18, 21, 21, 21, 21, 1, 1, 1, 1, 5, 5, 19, 19, 19, 19, 19, 1, 9, 9, 9, 21, 21, 21, 21, 21, 21, 1, 1, 1, 19, 1, 1] 56
rigid atoms, others: [32, 1, 34, 35, 9, 10, 11, 12, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 87
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071527 none CN(C(=O)C1(C)CC1F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', '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, 5, 5, 5, 15, 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]
dock color type numbers: [7, 7, 7, 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, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [8, 3, 1, 3, 1, 1, 1, 1, 1, 8, 21, 21, 21, 42, 42, 56, 56, 56, 56, 56, 21, 8, 8, 8, 2, 2, 2, 1, 1, 1, 21, 21, 21, 56, 21, 21] 56
rigid atoms, others: [2, 4, 5, 6, 7, 8, 27, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35])
total number of confs: 160
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071527 none CN(C(=O)C1(C)CC1F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', '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, 5, 5, 5, 15, 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]
dock color type numbers: [7, 7, 7, 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, 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: [42, 20, 42, 54, 54, 56, 56, 56, 56, 20, 19, 10, 1, 10, 1, 1, 1, 1, 1, 1, 19, 42, 42, 42, 56, 56, 56, 56, 56, 56, 20, 19, 19, 1, 19, 19] 56
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: 157
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071527 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071527
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071527/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071527
Building REAL250005071528
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071528'
/scratch/stefan/7916153/working/building/REAL250005071528 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071528

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071528/0 /scratch/stefan/7916153/working/building/REAL250005071528 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 662)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/662
`/scratch/stefan/7916153/working/3D/662' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C=CCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071528.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071528.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071528/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071528 none CN(C(=O)C=CCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 5, 15, 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]
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]
0  hydrogens 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, 24, 77, 126, 126, 189, 189, 201, 24, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 77, 77, 77, 189, 189, 201, 201, 24, 23, 24, 1, 24, 24] 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: 621
number of broken/clashed sets: 83
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071528 none CN(C(=O)C=CCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 5, 15, 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]
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]
0  hydrogens 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, 30, 30, 101, 101, 168, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 9, 9, 9, 101, 101, 168, 168, 1, 1, 1, 24, 1, 1] 201
rigid atoms, others: [32, 1, 8, 9, 10, 11, 19, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 639
number of broken/clashed sets: 83
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071528 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071528
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071528/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071528
Building REAL250005071529
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071529'
/scratch/stefan/7916153/working/building/REAL250005071529 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071529

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071529/0 /scratch/stefan/7916153/working/building/REAL250005071529 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 663)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/663
`/scratch/stefan/7916153/working/3D/663' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1(CO)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071529.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071529.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071529/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071529 none CN(C(=O)C1(CO)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 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]
1  hydrogens need rotated
306  conformations in input
total number of sets (complete confs): 306
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 24, 24, 30, 67, 30, 30, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 9, 9, 9, 67, 67, 201, 30, 30, 30, 30, 1, 1, 1, 17, 1, 1] 306
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 478
number of broken/clashed sets: 132
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071529 none CN(C(=O)C1(CO)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 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]
1  hydrogens need rotated
306  conformations in input
total number of sets (complete confs): 306
using faster count positions algorithm for large data
unique positions, atoms: [9, 3, 1, 3, 1, 1, 10, 1, 1, 9, 30, 30, 30, 67, 67, 94, 94, 94, 94, 94, 30, 9, 9, 9, 10, 10, 30, 1, 1, 1, 1, 30, 30, 30, 94, 30, 30] 306
rigid atoms, others: [2, 4, 5, 7, 8, 27, 28, 29, 30] set([0, 1, 3, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36])
total number of confs: 303
number of broken/clashed sets: 132
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071529 none CN(C(=O)C1(CO)CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 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]
1  hydrogens need rotated
306  conformations in input
total number of sets (complete confs): 306
using faster count positions algorithm for large data
unique positions, atoms: [54, 18, 54, 81, 81, 94, 102, 94, 94, 18, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 54, 54, 54, 102, 102, 306, 94, 94, 94, 94, 18, 17, 17, 1, 18, 18] 306
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: 132
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071529 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071529
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071529/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071529
Building REAL250005071530
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071530'
/scratch/stefan/7916153/working/building/REAL250005071530 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071530

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071530/0 /scratch/stefan/7916153/working/building/REAL250005071530 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 664)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/664
`/scratch/stefan/7916153/working/3D/664' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC=NO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071530.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071530.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071530/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071530 none CN(C(=O)C1=CC=NO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 1, 1, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 21, 21, 39, 39, 39, 39, 1, 1, 1, 1, 4, 4, 17, 17, 18, 17, 17, 1, 7, 7, 7, 39, 39, 1, 1, 1, 18, 1, 1] 60
rigid atoms, others: [1, 9, 10, 11, 12, 20, 26, 27, 28, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29])
total number of confs: 112
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071530 none CN(C(=O)C1=CC=NO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 1, 1, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [23, 10, 1, 10, 1, 1, 1, 1, 1, 23, 39, 39, 39, 55, 55, 60, 60, 60, 60, 60, 39, 23, 23, 23, 1, 1, 39, 39, 39, 60, 39, 39] 60
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 182
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071530 none CN(C(=O)C1=CC=NO1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 1, 1, 1, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [34, 18, 34, 50, 50, 60, 60, 60, 60, 18, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 34, 34, 34, 60, 60, 18, 17, 18, 1, 18, 17] 60
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 145
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071530 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071530
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071530/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071530
Building REAL250005071531
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071531'
/scratch/stefan/7916153/working/building/REAL250005071531 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL250005071531 as failed and skipping
/scratch/stefan/7916153/working /scratch/stefan/7916153
`/scratch/stefan/7916153/working/building/REAL250005071531' -> `/scratch/stefan/7916153/failed/REAL250005071531'
Building REAL250005071532
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071532'
/scratch/stefan/7916153/working/building/REAL250005071532 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071532

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071532/0 /scratch/stefan/7916153/working/building/REAL250005071532 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 665)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/665
`/scratch/stefan/7916153/working/3D/665' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071532.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071532.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071532/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071532 none C[C@H](O)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [59, 51, 59, 59, 37, 51, 16, 37, 16, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 59, 59, 59, 177, 37, 37, 37, 16, 16, 16, 1, 16, 16] 177
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: 365
number of broken/clashed sets: 53
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071532 none C[C@H](O)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [31, 18, 31, 31, 8, 18, 1, 8, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 31, 31, 31, 93, 8, 8, 8, 1, 1, 1, 16, 1, 1] 177
rigid atoms, others: [32, 6, 8, 9, 10, 11, 19, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 227
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071532 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071532
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071532/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071532
Building REAL250005071533
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071533'
/scratch/stefan/7916153/working/building/REAL250005071533 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071533

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071533/0 /scratch/stefan/7916153/working/building/REAL250005071533 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 666)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/666
`/scratch/stefan/7916153/working/3D/666' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071533.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071533.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071533/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071533 none CON=CC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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, 201, 146, 88, 146, 26, 88, 26, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 201, 201, 201, 201, 88, 88, 88, 26, 25, 26, 1, 26, 26] 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: 576
number of broken/clashed sets: 78
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071533 none CON=CC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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: [138, 103, 103, 31, 9, 31, 1, 9, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 138, 138, 138, 103, 9, 9, 9, 1, 1, 1, 26, 1, 1] 201
rigid atoms, others: [32, 6, 8, 9, 10, 11, 19, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 368
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071533 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071533
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071533/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071533
Building REAL250005071534
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071534'
/scratch/stefan/7916153/working/building/REAL250005071534 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071534

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071534/0 /scratch/stefan/7916153/working/building/REAL250005071534 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 667)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/667
`/scratch/stefan/7916153/working/3D/667' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[C@H](O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071534.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071534.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071534/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071534 none CC(C)[C@H](O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 7, 12, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
480  conformations in input
total number of sets (complete confs): 480
using faster count positions algorithm for large data
unique positions, atoms: [160, 141, 160, 102, 141, 141, 59, 102, 19, 59, 19, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 160, 160, 160, 160, 160, 160, 160, 423, 59, 59, 59, 19, 18, 18, 1, 19, 19] 480
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: 1003
number of broken/clashed sets: 244
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071534 none CC(C)[C@H](O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 7, 12, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
480  conformations in input
total number of sets (complete confs): 480
using faster count positions algorithm for large data
unique positions, atoms: [103, 71, 103, 31, 71, 71, 9, 31, 1, 9, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 103, 103, 103, 103, 103, 103, 103, 213, 9, 9, 9, 1, 1, 1, 18, 1, 1] 480
rigid atoms, others: [33, 34, 35, 37, 38, 8, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 691
number of broken/clashed sets: 244
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071534 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071534
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071534/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071534
Building REAL250005071535
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071535'
/scratch/stefan/7916153/working/building/REAL250005071535 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071535

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071535/0 /scratch/stefan/7916153/working/building/REAL250005071535 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 668)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/668
`/scratch/stefan/7916153/working/3D/668' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1)

`REAL250005071535.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071535.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071535/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071535 none C#CC1(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [42, 41, 27, 9, 27, 1, 9, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 42, 42, 42, 9, 9, 9, 1, 1, 1, 26, 1, 1, 42, 42, 42, 42] 100
rigid atoms, others: [5, 7, 8, 9, 10, 18, 25, 26, 27, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 28, 31, 32, 33, 34])
total number of confs: 165
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071535 none C#CC1(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 3, 3, 11, 11, 42, 42, 42, 78, 78, 100, 100, 100, 100, 100, 42, 1, 1, 1, 11, 11, 11, 42, 42, 42, 100, 42, 42, 1, 1, 1, 1] 100
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: 270
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071535 none C#CC1(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [100, 100, 79, 58, 79, 26, 58, 26, 25, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 100, 100, 100, 58, 58, 58, 26, 25, 26, 1, 26, 26, 100, 100, 100, 100] 100
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])
total number of confs: 295
number of broken/clashed sets: 40
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071535 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071535
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071535/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071535
Building REAL250005071536
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071536'
/scratch/stefan/7916153/working/building/REAL250005071536 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071536

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071536/0 /scratch/stefan/7916153/working/building/REAL250005071536 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 669)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/669
`/scratch/stefan/7916153/working/3D/669' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC=CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071536.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071536.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071536/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071536 none C=CC=CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 158, 66, 44, 66, 14, 44, 14, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 158, 158, 44, 44, 44, 14, 13, 14, 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: 733
number of broken/clashed sets: 91
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071536 none C=CC=CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [141, 141, 141, 69, 17, 9, 17, 1, 9, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 141, 141, 141, 141, 141, 69, 69, 9, 9, 9, 1, 1, 1, 14, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 7, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 495
number of broken/clashed sets: 91
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071536 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071536
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071536/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071536
Building REAL250005071537
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071537'
/scratch/stefan/7916153/working/building/REAL250005071537 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071537

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071537/0 /scratch/stefan/7916153/working/building/REAL250005071537 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 670)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/670
`/scratch/stefan/7916153/working/3D/670' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#C[C@H]1C[C@H]1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071537.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071537.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071537/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071537 none C#C[C@H]1C[C@H]1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 5, 7, 5, 5, 7, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [35, 35, 35, 35, 35, 20, 35, 7, 20, 1, 7, 1, 1, 1, 1, 4, 4, 16, 16, 16, 16, 16, 1, 35, 35, 35, 7, 7, 7, 1, 1, 1, 16, 1, 1] 59
rigid atoms, others: [33, 34, 9, 11, 12, 13, 14, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 121
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071537 none C#C[C@H]1C[C@H]1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 5, 7, 5, 5, 7, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 35, 35, 35, 51, 51, 59, 59, 59, 59, 59, 35, 1, 1, 1, 17, 17, 17, 35, 35, 35, 59, 35, 35] 59
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: 181
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071537 none C#C[C@H]1C[C@H]1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 5, 7, 5, 5, 7, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 59, 59, 52, 59, 34, 52, 16, 34, 16, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 59, 59, 59, 34, 34, 34, 16, 16, 16, 1, 16, 16] 59
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, 33, 34])
total number of confs: 161
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071537 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071537
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071537/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071537
Building REAL250005071538
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071538'
/scratch/stefan/7916153/working/building/REAL250005071538 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071538

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071538/0 /scratch/stefan/7916153/working/building/REAL250005071538 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 671)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/671
`/scratch/stefan/7916153/working/3D/671' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(CC)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071538.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071538.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071538/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071538 none CC=C(CC)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [186, 186, 131, 186, 201, 70, 131, 20, 70, 20, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 186, 186, 186, 186, 201, 201, 201, 201, 201, 70, 70, 70, 20, 19, 19, 1, 20, 19] 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: 642
number of broken/clashed sets: 79
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071538 none CC=C(CC)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 33, 78, 113, 9, 33, 1, 9, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 78, 78, 78, 78, 113, 113, 113, 113, 113, 9, 9, 9, 1, 1, 1, 19, 1, 1] 201
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 457
number of broken/clashed sets: 79
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071538 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071538
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071538/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071538
Building REAL250005071539
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071539'
/scratch/stefan/7916153/working/building/REAL250005071539 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071539

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071539/0 /scratch/stefan/7916153/working/building/REAL250005071539 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 672)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/672
`/scratch/stefan/7916153/working/3D/672' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(F)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071539.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071539.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071539/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071539 none COC(F)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 15, 1, 11, 8, 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]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [180, 172, 105, 172, 70, 105, 21, 70, 21, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 180, 180, 180, 172, 70, 70, 70, 21, 20, 20, 1, 21, 21] 180
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: 620
number of broken/clashed sets: 84
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071539 none COC(F)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 15, 1, 11, 8, 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]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [124, 67, 24, 67, 9, 24, 1, 9, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 124, 124, 124, 67, 9, 9, 9, 1, 1, 1, 20, 1, 1] 180
rigid atoms, others: [32, 6, 8, 9, 10, 11, 19, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 358
number of broken/clashed sets: 84
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071539 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071539
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071539/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071539
Building REAL250005071540
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071540'
/scratch/stefan/7916153/working/building/REAL250005071540 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071540

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071540/0 /scratch/stefan/7916153/working/building/REAL250005071540 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 673)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/673
`/scratch/stefan/7916153/working/3D/673' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071540.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071540.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071540/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071540 none COCC(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
588  conformations in input
total number of sets (complete confs): 588
using faster count positions algorithm for large data
unique positions, atoms: [196, 196, 165, 105, 165, 70, 105, 20, 70, 20, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 196, 196, 196, 196, 196, 165, 495, 70, 70, 70, 20, 19, 20, 1, 20, 20] 588
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: 1264
number of broken/clashed sets: 312
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071540 none COCC(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
588  conformations in input
total number of sets (complete confs): 588
using faster count positions algorithm for large data
unique positions, atoms: [138, 88, 48, 23, 48, 9, 23, 1, 9, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 138, 138, 138, 88, 88, 48, 144, 9, 9, 9, 1, 1, 1, 20, 1, 1] 588
rigid atoms, others: [32, 33, 35, 36, 7, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 646
number of broken/clashed sets: 312
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071540 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071540
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071540/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071540
Building REAL250005071541
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071541'
/scratch/stefan/7916153/working/building/REAL250005071541 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071541

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071541/0 /scratch/stefan/7916153/working/building/REAL250005071541 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 674)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/674
`/scratch/stefan/7916153/working/3D/674' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)[C@@H]1C[C@H]1C#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071541.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071541.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071541/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071541 none CN(C(=O)[C@@H]1C[C@H]1C#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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]
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, 1, 6, 19, 19, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 14, 1, 7, 7, 7, 52, 52, 1, 1, 1, 14, 1, 1] 87
rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 22, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31])
total number of confs: 175
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071541 none CN(C(=O)[C@@H]1C[C@H]1C#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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]
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: [26, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 26, 52, 52, 52, 80, 80, 87, 87, 87, 87, 87, 52, 26, 26, 26, 1, 1, 52, 52, 52, 87, 52, 52] 87
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 26, 27] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33])
total number of confs: 274
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071541 none CN(C(=O)[C@@H]1C[C@H]1C#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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]
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: [35, 15, 35, 55, 55, 87, 87, 87, 87, 87, 87, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 35, 35, 35, 87, 87, 15, 15, 15, 1, 14, 14] 87
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: 263
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071541 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071541
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071541/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071541
Building REAL250005071542
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071542'
/scratch/stefan/7916153/working/building/REAL250005071542 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071542

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071542/0 /scratch/stefan/7916153/working/building/REAL250005071542 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 675)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/675
`/scratch/stefan/7916153/working/3D/675' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)[C@H]1C[C@@H](O)C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071542.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071542.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071542/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071542 none CN(C(=O)[C@H]1C[C@@H](O)C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 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]
dock color type numbers: [7, 7, 7, 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]
1  hydrogens need rotated
303  conformations in input
total number of sets (complete confs): 303
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 21, 21, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 5, 5, 18, 18, 19, 18, 18, 1, 8, 8, 8, 51, 51, 153, 51, 51, 1, 1, 1, 18, 1, 1] 303
rigid atoms, others: [32, 1, 35, 36, 33, 11, 12, 13, 14, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 323
number of broken/clashed sets: 69
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071542 none CN(C(=O)[C@H]1C[C@@H](O)C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 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]
dock color type numbers: [7, 7, 7, 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]
1  hydrogens need rotated
303  conformations in input
total number of sets (complete confs): 303
using faster count positions algorithm for large data
unique positions, atoms: [26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 26, 51, 51, 51, 83, 83, 101, 101, 101, 101, 101, 51, 26, 26, 26, 1, 1, 3, 1, 1, 51, 51, 51, 101, 51, 51] 303
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 26, 27, 29, 30] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36])
total number of confs: 298
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071542 none CN(C(=O)[C@H]1C[C@@H](O)C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 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]
dock color type numbers: [7, 7, 7, 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]
1  hydrogens need rotated
303  conformations in input
total number of sets (complete confs): 303
using faster count positions algorithm for large data
unique positions, atoms: [50, 19, 50, 75, 75, 101, 101, 101, 101, 101, 101, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 101, 101, 303, 101, 101, 19, 18, 18, 1, 18, 18] 303
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: 603
number of broken/clashed sets: 69
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071542 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071542
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071542/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071542
Building REAL250005071543
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071543'
/scratch/stefan/7916153/working/building/REAL250005071543 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071543

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071543/0 /scratch/stefan/7916153/working/building/REAL250005071543 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 676)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/676
`/scratch/stefan/7916153/working/3D/676' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)COCCO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071543.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071543.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071543/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071543 none CN(C(=O)COCCO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 3, 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, 7]
1  hydrogens 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, 12, 44, 57, 57, 102, 161, 201, 201, 12, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 44, 44, 44, 102, 102, 201, 201, 201, 201, 603, 12, 11, 12, 1, 12, 12] 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: 1295
number of broken/clashed sets: 238
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071543 none CN(C(=O)COCCO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 3, 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, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 14, 14, 33, 80, 131, 146, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 1, 9, 9, 9, 33, 33, 131, 131, 146, 146, 438, 1, 1, 1, 12, 1, 1] 603
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 1003
number of broken/clashed sets: 238
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071543 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071543
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071543/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071543
Building REAL250005071544
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071544'
/scratch/stefan/7916153/working/building/REAL250005071544 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071544

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071544/0 /scratch/stefan/7916153/working/building/REAL250005071544 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 677)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/677
`/scratch/stefan/7916153/working/3D/677' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C(C)(C)CF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071544.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071544.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071544/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071544 none CN(C(=O)C(C)(C)CF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 15, 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, 7]
dock color type numbers: [7, 7, 7, 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, 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: [58, 21, 58, 68, 68, 77, 77, 77, 77, 21, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 58, 58, 58, 77, 77, 77, 77, 77, 77, 77, 77, 21, 20, 20, 1, 21, 21] 77
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: 213
number of broken/clashed sets: 77
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071544 none CN(C(=O)C(C)(C)CF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 15, 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, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 15, 15, 22, 22, 22, 35, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 9, 9, 9, 22, 22, 22, 22, 22, 22, 35, 35, 1, 1, 1, 20, 1, 1] 77
rigid atoms, others: [32, 1, 34, 36, 37, 33, 9, 10, 11, 12, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 184
number of broken/clashed sets: 77
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071544 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071544
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071544/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071544
Building REAL250005071545
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071545'
/scratch/stefan/7916153/working/building/REAL250005071545 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071545

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071545/0 /scratch/stefan/7916153/working/building/REAL250005071545 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 678)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/678
`/scratch/stefan/7916153/working/3D/678' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C(C)(C)CO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071545.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071545.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071545/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071545 none CN(C(=O)C(C)(C)CO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 12, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 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, 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: [37, 19, 37, 43, 43, 50, 50, 50, 50, 19, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 150, 19, 18, 18, 1, 19, 19] 150
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: 290
number of broken/clashed sets: 150
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071545 none CN(C(=O)C(C)(C)CO)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 12, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 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, 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: [9, 1, 9, 14, 14, 19, 19, 19, 30, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 9, 9, 9, 19, 19, 19, 19, 19, 19, 30, 30, 90, 1, 1, 1, 18, 1, 1] 150
rigid atoms, others: [1, 34, 35, 37, 38, 33, 9, 10, 11, 12, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 247
number of broken/clashed sets: 150
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071545 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071545
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071545/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071545
Building REAL250005071546
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071546'
/scratch/stefan/7916153/working/building/REAL250005071546 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071546

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071546/0 /scratch/stefan/7916153/working/building/REAL250005071546 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 679)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/679
`/scratch/stefan/7916153/working/3D/679' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071546.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071546.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071546/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071546 none C=CCC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 155, 97, 155, 70, 97, 21, 70, 21, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 201, 201, 201, 201, 201, 155, 155, 155, 155, 70, 70, 70, 21, 20, 21, 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: 832
number of broken/clashed sets: 104
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071546 none C=CCC(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 77, 36, 17, 36, 9, 17, 1, 9, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 129, 129, 129, 77, 77, 36, 36, 36, 36, 9, 9, 9, 1, 1, 1, 21, 1, 1] 201
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 547
number of broken/clashed sets: 104
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071546 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071546
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071546/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071546
Building REAL250005071547
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071547'
/scratch/stefan/7916153/working/building/REAL250005071547 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071547

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071547/0 /scratch/stefan/7916153/working/building/REAL250005071547 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 680)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/680
`/scratch/stefan/7916153/working/3D/680' -> `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)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071547.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071547.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071547/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071547 none C[C@@H]1C[C@H]1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [42, 42, 42, 42, 16, 42, 7, 16, 1, 7, 1, 1, 1, 1, 5, 5, 18, 18, 18, 18, 18, 1, 42, 42, 42, 42, 42, 7, 7, 7, 1, 1, 1, 18, 1, 1] 73
rigid atoms, others: [32, 34, 35, 8, 10, 11, 12, 13, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 141
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071547 none C[C@@H]1C[C@H]1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 26, 42, 42, 42, 66, 66, 73, 73, 73, 73, 73, 42, 2, 2, 2, 1, 1, 26, 26, 26, 42, 42, 42, 73, 42, 42] 73
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: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071547 none C[C@@H]1C[C@H]1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 73, 57, 73, 43, 57, 18, 43, 18, 18, 10, 1, 10, 1, 1, 1, 1, 1, 1, 18, 73, 73, 73, 73, 73, 43, 43, 43, 18, 18, 18, 1, 18, 18] 73
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: 216
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071547 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071547
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071547/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071547
Building REAL250005071548
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071548'
/scratch/stefan/7916153/working/building/REAL250005071548 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071548

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071548/0 /scratch/stefan/7916153/working/building/REAL250005071548 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 681)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/681
`/scratch/stefan/7916153/working/3D/681' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C(C)(C)O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071548.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071548.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071548/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071548 none CN(C(=O)C(C)(C)O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 12, 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]
dock color type numbers: [7, 7, 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, 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: [39, 21, 39, 50, 50, 59, 59, 59, 21, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 39, 39, 39, 59, 59, 59, 59, 59, 59, 177, 21, 20, 20, 1, 21, 21] 177
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: 351
number of broken/clashed sets: 105
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071548 none CN(C(=O)C(C)(C)O)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 12, 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]
dock color type numbers: [7, 7, 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, 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: [9, 1, 9, 19, 19, 27, 27, 27, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 9, 9, 9, 27, 27, 27, 27, 27, 27, 81, 1, 1, 1, 21, 1, 1] 177
rigid atoms, others: [32, 1, 34, 35, 8, 9, 10, 11, 19, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 208
number of broken/clashed sets: 105
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071548 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071548
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071548/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071548
Building REAL250005071549
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071549'
/scratch/stefan/7916153/working/building/REAL250005071549 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071549

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071549/0 /scratch/stefan/7916153/working/building/REAL250005071549 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 682)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/682
`/scratch/stefan/7916153/working/3D/682' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=NOCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071549.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071549.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071549/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071549 none CN(C(=O)C1=NOCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 8, 1, 11, 1, 8, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 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
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 32, 32, 74, 74, 74, 74, 1, 1, 1, 1, 7, 7, 22, 23, 23, 23, 23, 1, 9, 9, 9, 74, 74, 74, 74, 1, 1, 1, 23, 1, 1] 145
rigid atoms, others: [32, 1, 33, 9, 10, 11, 12, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 178
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071549 none CN(C(=O)C1=NOCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 8, 1, 11, 1, 8, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 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
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [34, 8, 1, 8, 1, 1, 1, 1, 1, 34, 74, 74, 74, 127, 127, 145, 145, 145, 145, 145, 74, 34, 34, 34, 1, 1, 1, 1, 74, 74, 74, 145, 74, 74] 145
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33])
total number of confs: 409
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071549 none CN(C(=O)C1=NOCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', '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']
dock atom type numbers: [5, 8, 1, 11, 1, 8, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 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
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [83, 23, 83, 123, 123, 145, 145, 145, 145, 23, 23, 11, 1, 11, 1, 1, 1, 1, 1, 1, 23, 83, 83, 83, 145, 145, 145, 145, 23, 23, 23, 1, 23, 23] 145
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])
total number of confs: 362
number of broken/clashed sets: 67
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071549 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071549
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071549/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071549
Building REAL250005071550
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071550'
/scratch/stefan/7916153/working/building/REAL250005071550 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071550

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071550/0 /scratch/stefan/7916153/working/building/REAL250005071550 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 683)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/683
`/scratch/stefan/7916153/working/3D/683' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C#N)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071550.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071550.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071550/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071550 none CC(C#N)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [115, 94, 115, 115, 56, 37, 56, 12, 37, 12, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 115, 115, 115, 115, 94, 94, 37, 37, 37, 12, 11, 12, 1, 12, 12] 115
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: 442
number of broken/clashed sets: 55
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071550 none CC(C#N)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [77, 55, 77, 77, 21, 9, 21, 1, 9, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 1, 77, 77, 77, 77, 55, 55, 9, 9, 9, 1, 1, 1, 12, 1, 1] 115
rigid atoms, others: [32, 34, 35, 7, 9, 10, 11, 12, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 339
number of broken/clashed sets: 55
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071550 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071550
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071550/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071550
Building REAL250005071551
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071551'
/scratch/stefan/7916153/working/building/REAL250005071551 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071551

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071551/0 /scratch/stefan/7916153/working/building/REAL250005071551 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 684)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/684
`/scratch/stefan/7916153/working/3D/684' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCO)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071551.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071551.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071551/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071551 none CC(CCO)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [173, 128, 173, 198, 201, 74, 128, 22, 74, 22, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 173, 173, 173, 173, 201, 201, 201, 198, 603, 74, 74, 74, 22, 21, 22, 1, 22, 22] 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: 1355
number of broken/clashed sets: 349
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071551 none CC(CCO)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [57, 29, 57, 89, 128, 9, 29, 1, 9, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 57, 57, 57, 57, 95, 95, 128, 123, 384, 9, 9, 9, 1, 1, 1, 22, 1, 1] 603
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 1033
number of broken/clashed sets: 349
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071551 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071551
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071551/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071551
Building REAL250005071552
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071552'
/scratch/stefan/7916153/working/building/REAL250005071552 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071552

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071552/0 /scratch/stefan/7916153/working/building/REAL250005071552 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 685)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/685
`/scratch/stefan/7916153/working/3D/685' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)[C@H](O)CF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071552.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071552.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071552/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071552 none CN(C(=O)[C@H](O)CF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 12, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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: [50, 15, 50, 85, 85, 122, 122, 122, 124, 15, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 366, 124, 124, 15, 14, 15, 1, 15, 15] 372
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: 806
number of broken/clashed sets: 173
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071552 none CN(C(=O)[C@H](O)CF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 12, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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: [9, 1, 9, 27, 27, 54, 54, 54, 92, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 9, 9, 9, 162, 92, 92, 1, 1, 1, 15, 1, 1] 372
rigid atoms, others: [32, 1, 9, 10, 11, 12, 20, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 587
number of broken/clashed sets: 173
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071552 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071552
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071552/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071552
Building REAL250005071553
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071553'
/scratch/stefan/7916153/working/building/REAL250005071553 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071553

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071553/0 /scratch/stefan/7916153/working/building/REAL250005071553 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 686)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/686
`/scratch/stefan/7916153/working/3D/686' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1(O)CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071553.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071553.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071553/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071553 none CN(C(=O)C1(O)CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 12, 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, 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]
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: [9, 1, 9, 23, 23, 35, 35, 35, 35, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 9, 9, 9, 105, 35, 35, 35, 35, 35, 35, 1, 1, 1, 23, 1, 1] 234
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 238
number of broken/clashed sets: 90
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071553 none CN(C(=O)C1(O)CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 12, 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, 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]
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: [16, 7, 1, 6, 1, 1, 1, 1, 1, 16, 35, 35, 35, 62, 62, 78, 78, 78, 78, 78, 35, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 35, 35, 35, 78, 35, 35] 234
rigid atoms, others: [2, 4, 5, 6, 7, 8, 25, 26, 27, 28, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36])
total number of confs: 226
number of broken/clashed sets: 90
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071553 none CN(C(=O)C1(O)CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 12, 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, 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]
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: [48, 23, 48, 68, 68, 78, 78, 78, 78, 23, 23, 11, 1, 11, 1, 1, 1, 1, 1, 1, 23, 48, 48, 48, 234, 78, 78, 78, 78, 78, 78, 23, 23, 23, 1, 23, 23] 234
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: 450
number of broken/clashed sets: 90
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071553 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071553
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071553/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071553
Building REAL250005071554
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071554'
/scratch/stefan/7916153/working/building/REAL250005071554 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071554

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071554/0 /scratch/stefan/7916153/working/building/REAL250005071554 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 687)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/687
`/scratch/stefan/7916153/working/3D/687' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C(O)C1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071554.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071554.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071554/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071554 none CN(C(=O)C(O)C1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 12, 5, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
1  hydrogens need rotated
414  conformations in input
total number of sets (complete confs): 414
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 21, 21, 49, 49, 86, 86, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 7, 7, 7, 49, 147, 86, 86, 86, 86, 86, 1, 1, 1, 25, 1, 1] 414
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 496
number of broken/clashed sets: 69
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071554 none CN(C(=O)C(O)C1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 12, 5, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
1  hydrogens need rotated
414  conformations in input
total number of sets (complete confs): 414
using faster count positions algorithm for large data
unique positions, atoms: [52, 29, 6, 29, 1, 6, 1, 1, 1, 52, 86, 86, 86, 129, 129, 138, 138, 138, 138, 138, 86, 52, 52, 52, 6, 18, 1, 1, 1, 1, 1, 86, 86, 86, 138, 86, 86] 414
rigid atoms, others: [4, 6, 7, 8, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36])
total number of confs: 458
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071554 none CN(C(=O)C(O)C1CC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 12, 5, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
1  hydrogens need rotated
414  conformations in input
total number of sets (complete confs): 414
using faster count positions algorithm for large data
unique positions, atoms: [51, 25, 51, 91, 91, 121, 121, 138, 138, 25, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 51, 51, 51, 121, 363, 138, 138, 138, 138, 138, 25, 24, 25, 1, 25, 25] 414
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: 840
number of broken/clashed sets: 69
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071554 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071554
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071554/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071554
Building REAL250005071555
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071555'
/scratch/stefan/7916153/working/building/REAL250005071555 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071555

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071555/0 /scratch/stefan/7916153/working/building/REAL250005071555 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 688)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/688
`/scratch/stefan/7916153/working/3D/688' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071555.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071555.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071555/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071555 none C=C(C)CC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 69, 113, 19, 69, 19, 18, 5, 1, 5, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 201, 201, 201, 69, 69, 69, 19, 18, 19, 1, 19, 19] 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: 100
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071555 none C=C(C)CC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 101, 134, 26, 9, 26, 1, 9, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 134, 134, 134, 134, 134, 101, 101, 9, 9, 9, 1, 1, 1, 19, 1, 1] 201
rigid atoms, others: [32, 34, 35, 6, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 507
number of broken/clashed sets: 100
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071555 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071555
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071555/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071555
Building REAL250005071556
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071556'
/scratch/stefan/7916153/working/building/REAL250005071556 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071556

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071556/0 /scratch/stefan/7916153/working/building/REAL250005071556 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 689)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/689
`/scratch/stefan/7916153/working/3D/689' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C(C)(C)C#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071556.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071556.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071556/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071556 none CN(C(=O)C(C)(C)C#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 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, 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: [39, 22, 39, 42, 42, 42, 42, 42, 42, 22, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 39, 39, 39, 42, 42, 42, 42, 42, 42, 22, 21, 21, 1, 22, 21] 42
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: 102
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071556 none CN(C(=O)C(C)(C)C#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 1, 8, 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]
dock color type numbers: [7, 7, 7, 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, 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: [9, 1, 9, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 9, 9, 9, 15, 15, 15, 15, 15, 15, 1, 1, 1, 21, 1, 1] 42
rigid atoms, others: [32, 1, 34, 35, 9, 10, 11, 12, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 70
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071556 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071556
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071556/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071556
Building REAL250005071557
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071557'
/scratch/stefan/7916153/working/building/REAL250005071557 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071557

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071557/0 /scratch/stefan/7916153/working/building/REAL250005071557 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 690)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/690
`/scratch/stefan/7916153/working/3D/690' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCSCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071557.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071557.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071557/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071557 none CCSCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 14, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 179, 128, 77, 47, 77, 14, 47, 14, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 128, 128, 47, 47, 47, 14, 13, 14, 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: 675
number of broken/clashed sets: 102
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071557 none CCSCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 14, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [147, 110, 52, 22, 9, 22, 1, 9, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 147, 147, 147, 147, 147, 52, 52, 9, 9, 9, 1, 1, 1, 14, 1, 1] 201
rigid atoms, others: [32, 34, 35, 6, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 521
number of broken/clashed sets: 102
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071557 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071557
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071557/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071557
Building REAL250005071558
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071558'
/scratch/stefan/7916153/working/building/REAL250005071558 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071558

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071558/0 /scratch/stefan/7916153/working/building/REAL250005071558 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 691)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/691
`/scratch/stefan/7916153/working/3D/691' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=C(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071558.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071558.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071558/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071558 none CC(C)=C(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 63, 77, 25, 63, 25, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 103, 103, 103, 103, 103, 103, 103, 103, 103, 63, 63, 63, 25, 24, 24, 1, 25, 25] 103
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: 308
number of broken/clashed sets: 49
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071558 none CC(C)=C(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 37, 37, 24, 37, 9, 24, 1, 9, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 25, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 9, 9, 9, 1, 1, 1, 25, 1, 1] 103
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 150
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071558 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071558
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071558/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071558
Building REAL250005071559
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071559'
/scratch/stefan/7916153/working/building/REAL250005071559 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071559

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071559/0 /scratch/stefan/7916153/working/building/REAL250005071559 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 692)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/692
`/scratch/stefan/7916153/working/3D/692' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071559.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071559.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071559/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071559 none CNC(=O)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 1, 11, 8, 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]
dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [154, 154, 127, 154, 63, 43, 63, 11, 43, 11, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 154, 154, 154, 154, 127, 127, 43, 43, 43, 11, 10, 11, 1, 11, 11] 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: 571
number of broken/clashed sets: 90
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071559 none CNC(=O)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 1, 11, 8, 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]
dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 63, 104, 19, 9, 19, 1, 9, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 1, 104, 104, 104, 104, 63, 63, 9, 9, 9, 1, 1, 1, 11, 1, 1] 154
rigid atoms, others: [32, 34, 35, 7, 9, 10, 11, 12, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 385
number of broken/clashed sets: 90
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071559 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071559
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071559/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071559
Building REAL250005071560
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071560'
/scratch/stefan/7916153/working/building/REAL250005071560 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071560

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071560/0 /scratch/stefan/7916153/working/building/REAL250005071560 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 693)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/693
`/scratch/stefan/7916153/working/3D/693' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1CC(F)C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071560.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071560.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071560/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071560 none CN(C(=O)C1CC(F)C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 15, 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]
dock color type numbers: [7, 7, 7, 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, 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: [8, 1, 8, 21, 21, 50, 50, 50, 50, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 8, 8, 8, 50, 50, 50, 50, 50, 50, 1, 1, 1, 20, 1, 1] 96
rigid atoms, others: [32, 1, 34, 35, 9, 10, 11, 12, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 172
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071560 none CN(C(=O)C1CC(F)C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 15, 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]
dock color type numbers: [7, 7, 7, 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, 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: [26, 8, 1, 8, 1, 1, 1, 1, 1, 26, 50, 50, 50, 83, 83, 96, 96, 96, 96, 96, 50, 26, 26, 26, 1, 1, 1, 1, 1, 1, 50, 50, 50, 96, 50, 50] 96
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35])
total number of confs: 287
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071560 none CN(C(=O)C1CC(F)C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 15, 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]
dock color type numbers: [7, 7, 7, 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, 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: [48, 20, 48, 71, 71, 96, 96, 96, 96, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 48, 48, 48, 96, 96, 96, 96, 96, 96, 20, 20, 20, 1, 20, 20] 96
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: 275
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071560 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071560
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071560/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071560
Building REAL250005071561
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071561'
/scratch/stefan/7916153/working/building/REAL250005071561 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071561

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071561/0 /scratch/stefan/7916153/working/building/REAL250005071561 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 694)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/694
`/scratch/stefan/7916153/working/3D/694' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071561.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071561.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071561/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071561 none C=CCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 110, 81, 110, 22, 81, 22, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 22, 188, 188, 188, 188, 188, 81, 81, 81, 22, 21, 22, 1, 22, 22] 188
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: 696
number of broken/clashed sets: 90
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071561 none C=CCC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [126, 78, 19, 9, 19, 1, 9, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 126, 126, 126, 78, 78, 9, 9, 9, 1, 1, 1, 22, 1, 1] 188
rigid atoms, others: [32, 5, 7, 8, 9, 10, 18, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 474
number of broken/clashed sets: 90
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071561 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071561
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071561/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071561
Building REAL250005071562
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071562'
/scratch/stefan/7916153/working/building/REAL250005071562 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071562

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071562/0 /scratch/stefan/7916153/working/building/REAL250005071562 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 695)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/695
`/scratch/stefan/7916153/working/3D/695' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C[NH+](C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071562.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071562.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071562/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071562 none CN(C(=O)C[NH+](C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', '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, 8, 1, 11, 5, 9, 6, 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, 7]
dock color type numbers: [7, 7, 7, 6, 7, 1, 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
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [10, 8, 10, 10, 10, 10, 10, 10, 10, 8, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 7, 8, 1, 8, 8] 10
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: 26
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071562 none CN(C(=O)C[NH+](C)C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', '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, 8, 1, 11, 5, 9, 6, 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, 7]
dock color type numbers: [7, 7, 7, 6, 7, 1, 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
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 5, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 8, 1, 1] 10
rigid atoms, others: [32, 1, 34, 36, 37, 33, 9, 10, 11, 12, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 37
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071562 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071562/1 /scratch/stefan/7916153/working/building/REAL250005071562 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 696)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/696
`/scratch/stefan/7916153/working/3D/696' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071562.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071562.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071562/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071562 none CN(C)CC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [166, 161, 166, 106, 72, 106, 24, 72, 24, 23, 11, 1, 11, 1, 1, 1, 1, 1, 1, 24, 166, 166, 166, 166, 166, 166, 161, 161, 72, 72, 72, 24, 23, 24, 1, 24, 24] 166
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])
total number of confs: 556
number of broken/clashed sets: 77
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071562 none CN(C)CC(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [109, 89, 109, 29, 9, 29, 1, 9, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 109, 109, 109, 109, 109, 109, 89, 89, 9, 9, 9, 1, 1, 1, 24, 1, 1] 166
rigid atoms, others: [32, 33, 35, 36, 6, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 421
number of broken/clashed sets: 77
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071562 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071562
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071562/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071562/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071562
Building REAL250005071563
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071563'
/scratch/stefan/7916153/working/building/REAL250005071563 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071563

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071563/0 /scratch/stefan/7916153/working/building/REAL250005071563 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 697)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/697
`/scratch/stefan/7916153/working/3D/697' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CC#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071563.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071563.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071563/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071563 none CN(C(=O)CC#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 5, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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]
0  hydrogens need rotated
161  conformations in input
total number of sets (complete confs): 161
using faster count positions algorithm for large data
unique positions, atoms: [81, 26, 81, 118, 118, 161, 161, 26, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 81, 81, 81, 161, 161, 26, 25, 26, 1, 26, 26] 161
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])
total number of confs: 552
number of broken/clashed sets: 62
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071563 none CN(C(=O)CC#N)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 11, 5, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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]
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: [9, 1, 9, 28, 28, 80, 80, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 9, 9, 9, 80, 80, 1, 1, 1, 27, 1, 1] 162
rigid atoms, others: [1, 7, 8, 9, 10, 18, 24, 25, 26, 28, 29] set([0, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 27])
total number of confs: 328
number of broken/clashed sets: 62
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071563 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071563
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071563/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071563
Building REAL250005071564
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071564'
/scratch/stefan/7916153/working/building/REAL250005071564 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071564

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071564/0 /scratch/stefan/7916153/working/building/REAL250005071564 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 698)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/698
`/scratch/stefan/7916153/working/3D/698' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1CC1F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071564.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071564.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071564/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071564 none CN(C(=O)C1CC1F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 15, 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]
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]
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, 14, 14, 31, 31, 31, 1, 1, 1, 1, 4, 4, 16, 16, 16, 16, 16, 1, 7, 7, 7, 31, 31, 31, 31, 1, 1, 1, 17, 1, 1] 59
rigid atoms, others: [32, 1, 8, 9, 10, 11, 19, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 115
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071564 none CN(C(=O)C1CC1F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 15, 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]
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]
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: [21, 8, 1, 8, 1, 1, 1, 1, 21, 31, 31, 31, 48, 48, 59, 59, 59, 59, 59, 31, 21, 21, 21, 1, 1, 1, 1, 31, 31, 31, 59, 31, 31] 59
rigid atoms, others: [2, 4, 5, 6, 7, 23, 24, 25, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32])
total number of confs: 172
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071564 none CN(C(=O)C1CC1F)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 15, 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]
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]
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: [30, 17, 30, 41, 41, 59, 59, 59, 17, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 30, 30, 30, 59, 59, 59, 59, 17, 16, 17, 1, 17, 17] 59
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: 175
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071564 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071564
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071564/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071564
Building REAL250005071565
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071565'
/scratch/stefan/7916153/working/building/REAL250005071565 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071565

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071565/0 /scratch/stefan/7916153/working/building/REAL250005071565 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 699)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/699
`/scratch/stefan/7916153/working/3D/699' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C)

`REAL250005071565.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071565.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071565/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071565 none C[C@@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 7, 3, 7, 3, 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
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 20, 16, 20, 7, 16, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 20, 21, 21, 21, 20, 20, 20, 16, 16, 16, 7, 7, 7, 1, 7, 7, 21, 21, 21, 21, 21, 21] 21
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, 39, 40])
total number of confs: 57
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071565 none C[C@@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 7, 3, 7, 3, 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
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [12, 10, 12, 7, 10, 1, 7, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 1, 12, 14, 14, 14, 12, 12, 12, 7, 7, 7, 1, 1, 1, 7, 1, 1, 14, 14, 14, 14, 14, 14] 21
rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 35, 36, 37, 38, 39, 40])
total number of confs: 65
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071565 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071565/1 /scratch/stefan/7916153/working/building/REAL250005071565 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 700)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/700
`/scratch/stefan/7916153/working/3D/700' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C)

`REAL250005071565.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071565.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071565/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071565 none C[C@@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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: [130, 107, 130, 63, 107, 18, 63, 18, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 130, 133, 133, 130, 130, 130, 63, 63, 63, 18, 17, 18, 1, 18, 18, 133, 133, 133, 133, 133, 133] 133
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, 39])
total number of confs: 426
number of broken/clashed sets: 69
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071565 none C[C@@H](C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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: [66, 29, 66, 9, 29, 1, 9, 1, 1, 1, 1, 6, 6, 17, 17, 17, 18, 18, 1, 66, 82, 82, 66, 66, 66, 9, 9, 9, 1, 1, 1, 18, 1, 1, 82, 82, 82, 82, 82, 82] 133
rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 34, 35, 36, 37, 38, 39])
total number of confs: 341
number of broken/clashed sets: 69
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071565 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071565
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071565/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071565/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071565
Building REAL250005071566
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071566'
/scratch/stefan/7916153/working/building/REAL250005071566 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071566

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071566/0 /scratch/stefan/7916153/working/building/REAL250005071566 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 701)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/701
`/scratch/stefan/7916153/working/3D/701' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071566.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071566.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071566/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071566 none CN(C(=O)CCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 15, 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]
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]
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: [78, 24, 78, 120, 120, 179, 181, 24, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 78, 78, 78, 179, 179, 181, 181, 24, 23, 24, 1, 24, 24] 181
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])
total number of confs: 621
number of broken/clashed sets: 84
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071566 none CN(C(=O)CCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 15, 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]
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]
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: [9, 1, 9, 25, 25, 81, 115, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 9, 9, 9, 81, 81, 115, 115, 1, 1, 1, 24, 1, 1] 181
rigid atoms, others: [1, 7, 8, 9, 10, 18, 26, 27, 28, 30, 31] set([0, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29])
total number of confs: 508
number of broken/clashed sets: 84
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071566 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071566
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071566/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071566
Building REAL250005071567
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071567'
/scratch/stefan/7916153/working/building/REAL250005071567 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071567

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071567/0 /scratch/stefan/7916153/working/building/REAL250005071567 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 702)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/702
`/scratch/stefan/7916153/working/3D/702' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1C=CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071567.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071567.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071567/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071567 none CN(C(=O)C1C=CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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, 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, 16, 16, 32, 32, 32, 32, 1, 1, 1, 1, 5, 5, 18, 18, 18, 18, 18, 1, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 18, 1, 1] 78
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 114
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071567 none CN(C(=O)C1C=CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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, 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: [20, 6, 1, 6, 1, 1, 1, 1, 1, 20, 32, 32, 32, 56, 56, 78, 78, 78, 78, 78, 32, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 78, 32, 32] 78
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36])
total number of confs: 227
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071567 none CN(C(=O)C1C=CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 1, 1, 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]
dock color type numbers: [7, 7, 7, 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, 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, 19, 41, 60, 60, 78, 78, 78, 78, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 41, 41, 41, 78, 78, 78, 78, 78, 78, 78, 19, 18, 18, 1, 18, 18] 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])
total number of confs: 248
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071567 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071567
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071567/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071567
Building REAL250005071568
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071568'
/scratch/stefan/7916153/working/building/REAL250005071568 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071568

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071568/0 /scratch/stefan/7916153/working/building/REAL250005071568 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 703)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/703
`/scratch/stefan/7916153/working/3D/703' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC(C)(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071568.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071568.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071568/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071568 none C#CC(C)(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [50, 50, 50, 50, 50, 44, 50, 23, 44, 23, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 23, 22, 23, 1, 23, 23] 50
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: 123
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071568 none C#CC(C)(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 17, 9, 17, 1, 9, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 1, 1, 1, 23, 1, 1] 50
rigid atoms, others: [32, 33, 35, 36, 7, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 80
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071568 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071568
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071568/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071568
Building REAL250005071569
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071569'
/scratch/stefan/7916153/working/building/REAL250005071569 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071569

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071569/0 /scratch/stefan/7916153/working/building/REAL250005071569 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 704)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/704
`/scratch/stefan/7916153/working/3D/704' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CO[C@H](C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071569.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071569.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071569/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071569 none CO[C@H](C)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [79, 79, 62, 79, 79, 41, 62, 12, 41, 12, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 79, 79, 79, 79, 79, 79, 41, 41, 41, 12, 11, 12, 1, 12, 12] 79
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: 263
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071569 none CO[C@H](C)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 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]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [51, 42, 22, 42, 42, 9, 22, 1, 9, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 1, 51, 51, 51, 42, 42, 42, 9, 9, 9, 1, 1, 1, 12, 1, 1] 79
rigid atoms, others: [32, 34, 35, 7, 9, 10, 11, 12, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 191
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071569 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071569
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071569/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071569
Building REAL250005071570
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071570'
/scratch/stefan/7916153/working/building/REAL250005071570 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071570

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071570/0 /scratch/stefan/7916153/working/building/REAL250005071570 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 705)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/705
`/scratch/stefan/7916153/working/3D/705' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071570.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071570.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071570/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071570 none CC(=O)CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 20, 15, 9, 9, 9, 6, 9, 6, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 15, 15, 15, 15, 9, 9, 9, 6, 5, 6, 1, 6, 6] 20
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: 74
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071570 none CC(=O)CCC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [19, 11, 19, 10, 5, 5, 5, 1, 5, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 1, 19, 19, 19, 11, 11, 10, 10, 5, 5, 5, 1, 1, 1, 6, 1, 1] 20
rigid atoms, others: [32, 33, 35, 36, 7, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 76
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071570 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071570
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071570/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071570
Building REAL250005071571
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071571'
/scratch/stefan/7916153/working/building/REAL250005071571 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071571

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071571/0 /scratch/stefan/7916153/working/building/REAL250005071571 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 706)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/706
`/scratch/stefan/7916153/working/3D/706' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071571.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071571.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071571/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071571 none C[C@@H](O)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
252  conformations in input
total number of sets (complete confs): 252
using faster count positions algorithm for large data
unique positions, atoms: [84, 77, 84, 84, 56, 77, 22, 56, 22, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 84, 84, 84, 252, 56, 56, 56, 22, 21, 22, 1, 22, 22] 252
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: 503
number of broken/clashed sets: 126
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071571 none C[C@@H](O)C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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
252  conformations in input
total number of sets (complete confs): 252
using faster count positions algorithm for large data
unique positions, atoms: [44, 23, 44, 44, 9, 23, 1, 9, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 44, 44, 44, 132, 9, 9, 9, 1, 1, 1, 22, 1, 1] 252
rigid atoms, others: [32, 6, 8, 9, 10, 11, 19, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 335
number of broken/clashed sets: 126
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071571 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071571
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071571/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071571
Building REAL250005071572
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071572'
/scratch/stefan/7916153/working/building/REAL250005071572 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071572

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071572/0 /scratch/stefan/7916153/working/building/REAL250005071572 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 707)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/707
`/scratch/stefan/7916153/working/3D/707' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CN1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071572.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071572.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071572/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071572 none CN(C(=O)CN1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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']
dock atom type numbers: [5, 8, 1, 11, 5, 10, 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, 7]
dock color type numbers: [7, 7, 7, 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, 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: [9, 1, 9, 32, 32, 94, 118, 118, 118, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 9, 9, 9, 94, 94, 118, 118, 118, 118, 118, 118, 1, 1, 1, 22, 1, 1] 181
rigid atoms, others: [32, 1, 34, 36, 37, 33, 9, 10, 11, 12, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 411
number of broken/clashed sets: 83
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071572 none CN(C(=O)CN1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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']
dock atom type numbers: [5, 8, 1, 11, 5, 10, 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, 7]
dock color type numbers: [7, 7, 7, 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, 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: [66, 25, 6, 25, 1, 1, 1, 1, 1, 66, 118, 118, 118, 171, 171, 181, 181, 181, 181, 181, 118, 66, 66, 66, 6, 6, 1, 1, 1, 1, 1, 1, 118, 118, 118, 181, 118, 118] 181
rigid atoms, others: [4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37])
total number of confs: 554
number of broken/clashed sets: 83
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071572 none CN(C(=O)CN1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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']
dock atom type numbers: [5, 8, 1, 11, 5, 10, 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, 7]
dock color type numbers: [7, 7, 7, 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, 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: [70, 22, 70, 121, 121, 176, 181, 181, 181, 22, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 70, 70, 70, 176, 176, 181, 181, 181, 181, 181, 181, 22, 21, 22, 1, 22, 22] 181
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: 595
number of broken/clashed sets: 83
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071572 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071572/1 /scratch/stefan/7916153/working/building/REAL250005071572 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 708)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/708
`/scratch/stefan/7916153/working/3D/708' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C[NH+]1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071572.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071572.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071572/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071572 none CN(C(=O)C[NH+]1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', '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, 8, 1, 11, 5, 9, 6, 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, 7]
dock color type numbers: [7, 7, 7, 6, 7, 1, 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
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 1, 1, 1, 5, 1, 1] 9
rigid atoms, others: [1, 34, 35, 37, 38, 33, 10, 11, 12, 13, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 29
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071572 none CN(C(=O)C[NH+]1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', '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, 8, 1, 11, 5, 9, 6, 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, 7]
dock color type numbers: [7, 7, 7, 6, 7, 1, 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
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 7, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 7, 7] 9
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36, 37, 38])
total number of confs: 32
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071572 none CN(C(=O)C[NH+]1CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', '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, 8, 1, 11, 5, 9, 6, 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, 7]
dock color type numbers: [7, 7, 7, 6, 7, 1, 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
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 5, 9, 9, 9, 9, 9, 9, 9, 9, 5, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 4, 5, 1, 5, 5] 9
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: 27
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071572 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071572
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071572/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071572/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071572
Building REAL250005071573
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071573'
/scratch/stefan/7916153/working/building/REAL250005071573 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071573

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071573/0 /scratch/stefan/7916153/working/building/REAL250005071573 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 709)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/709
`/scratch/stefan/7916153/working/3D/709' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071573.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071573.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071573/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071573 none CC(O)C(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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
360  conformations in input
total number of sets (complete confs): 360
using faster count positions algorithm for large data
unique positions, atoms: [119, 108, 120, 85, 108, 58, 85, 19, 58, 19, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 120, 120, 120, 120, 360, 108, 108, 108, 108, 58, 58, 58, 19, 18, 19, 1, 19, 19] 360
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: 781
number of broken/clashed sets: 181
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071573 none CC(O)C(C)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 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
360  conformations in input
total number of sets (complete confs): 360
using faster count positions algorithm for large data
unique positions, atoms: [88, 54, 89, 27, 54, 9, 27, 1, 9, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 89, 89, 89, 89, 267, 54, 54, 54, 54, 9, 9, 9, 1, 1, 1, 19, 1, 1] 360
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 684
number of broken/clashed sets: 181
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071573 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071573
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071573/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071573
Building REAL250005071574
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071574'
/scratch/stefan/7916153/working/building/REAL250005071574 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071574

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071574/0 /scratch/stefan/7916153/working/building/REAL250005071574 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 710)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/710
`/scratch/stefan/7916153/working/3D/710' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071574.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071574.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071574/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071574 none C=C1CC1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [64, 64, 64, 26, 9, 26, 1, 9, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 64, 64, 64, 64, 64, 9, 9, 9, 1, 1, 1, 25, 1, 1] 132
rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 217
number of broken/clashed sets: 54
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071574 none C=C1CC1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 24, 24, 64, 64, 64, 116, 116, 132, 132, 132, 132, 132, 64, 1, 1, 1, 1, 1, 24, 24, 24, 64, 64, 64, 132, 64, 64] 132
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: 379
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071574 none C=C1CC1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 132, 132, 96, 68, 96, 25, 68, 25, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 132, 132, 132, 132, 132, 68, 68, 68, 25, 24, 25, 1, 25, 25] 132
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: 396
number of broken/clashed sets: 54
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071574 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071574
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071574/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071574
Building REAL250005071575
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071575'
/scratch/stefan/7916153/working/building/REAL250005071575 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071575

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071575/0 /scratch/stefan/7916153/working/building/REAL250005071575 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 711)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/711
`/scratch/stefan/7916153/working/3D/711' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(OC)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071575.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071575.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071575/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071575 none COC(OC)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 5, 1, 11, 8, 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]
dock color type numbers: [7, 3, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 93, 149, 201, 57, 93, 19, 57, 19, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 201, 201, 201, 149, 201, 201, 201, 57, 57, 57, 19, 18, 18, 1, 19, 19] 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: 718
number of broken/clashed sets: 86
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071575 none COC(OC)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 5, 1, 11, 8, 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]
dock color type numbers: [7, 3, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 53, 25, 53, 113, 9, 25, 1, 9, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 115, 115, 115, 53, 113, 113, 113, 9, 9, 9, 1, 1, 1, 18, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 7, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 402
number of broken/clashed sets: 86
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071575 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071575
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071575/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071575
Building REAL250005071576
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071576'
/scratch/stefan/7916153/working/building/REAL250005071576 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071576

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071576/0 /scratch/stefan/7916153/working/building/REAL250005071576 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 712)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/712
`/scratch/stefan/7916153/working/3D/712' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1(C)COC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071576.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071576.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071576/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071576 none CN(C(=O)C1(C)COC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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: [9, 1, 9, 18, 18, 19, 19, 19, 19, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 1, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 12, 1, 1] 40
rigid atoms, others: [32, 1, 35, 36, 33, 9, 10, 11, 12, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34])
total number of confs: 68
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071576 none CN(C(=O)C1(C)COC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [8, 4, 1, 4, 1, 1, 1, 1, 1, 8, 19, 19, 19, 34, 34, 40, 40, 40, 40, 40, 19, 8, 8, 8, 2, 2, 2, 1, 1, 1, 1, 19, 19, 19, 40, 19, 19] 40
rigid atoms, others: [2, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36])
total number of confs: 122
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071576 none CN(C(=O)C1(C)COC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 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, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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, 13, 28, 39, 39, 40, 40, 40, 40, 13, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 28, 28, 28, 40, 40, 40, 40, 40, 40, 40, 13, 12, 12, 1, 13, 13] 40
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: 104
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071576 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071576
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071576/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071576
Building REAL250005071577
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071577'
/scratch/stefan/7916153/working/building/REAL250005071577 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071577

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071577/0 /scratch/stefan/7916153/working/building/REAL250005071577 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 713)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/713
`/scratch/stefan/7916153/working/3D/713' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1CC(=O)N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071577.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071577.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071577/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071577 none CN(C(=O)C1CC(=O)N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 6, 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]
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: [7, 1, 7, 21, 21, 53, 53, 53, 53, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 8, 8, 8, 53, 53, 53, 53, 1, 1, 1, 19, 1, 1] 96
rigid atoms, others: [32, 1, 33, 9, 10, 11, 12, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 184
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071577 none CN(C(=O)C1CC(=O)N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 6, 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]
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: [25, 8, 1, 8, 1, 1, 1, 1, 1, 25, 53, 53, 53, 87, 87, 96, 96, 96, 96, 96, 53, 25, 25, 25, 1, 1, 1, 1, 53, 53, 53, 96, 53, 53] 96
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33])
total number of confs: 290
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071577 none CN(C(=O)C1CC(=O)N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 6, 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]
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: [46, 20, 46, 73, 73, 96, 96, 96, 96, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 46, 46, 46, 96, 96, 96, 96, 20, 20, 20, 1, 19, 19] 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])
total number of confs: 285
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071577 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071577
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071577/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071577
Building REAL250005071578
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071578'
/scratch/stefan/7916153/working/building/REAL250005071578 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071578

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071578/0 /scratch/stefan/7916153/working/building/REAL250005071578 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 714)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/714
`/scratch/stefan/7916153/working/3D/714' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)[C@@H]1CC(=O)N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071578.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071578.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071578/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071578 none CN(C(=O)[C@@H]1CC(=O)N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 6, 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]
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, 22, 22, 49, 49, 49, 49, 49, 1, 1, 1, 1, 5, 5, 19, 19, 19, 19, 19, 1, 7, 7, 7, 49, 49, 49, 1, 1, 1, 20, 1, 1] 102
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 21, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 169
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071578 none CN(C(=O)[C@@H]1CC(=O)N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 6, 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]
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: [24, 6, 1, 6, 1, 1, 1, 1, 1, 1, 24, 49, 49, 49, 79, 79, 102, 102, 102, 102, 102, 49, 24, 24, 24, 1, 1, 1, 49, 49, 49, 102, 49, 49] 102
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33])
total number of confs: 291
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071578 none CN(C(=O)[C@@H]1CC(=O)N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 6, 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]
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: [46, 20, 46, 77, 77, 102, 102, 102, 102, 102, 20, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 46, 46, 46, 102, 102, 102, 20, 19, 20, 1, 20, 20] 102
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: 318
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071578 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071578
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071578/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071578
Building REAL250005071579
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071579'
/scratch/stefan/7916153/working/building/REAL250005071579 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071579

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071579/0 /scratch/stefan/7916153/working/building/REAL250005071579 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 715)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/715
`/scratch/stefan/7916153/working/3D/715' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC[C@H](O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071579.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071579.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071579/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071579 none CCC[C@H](O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 7, 12, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 198, 144, 95, 144, 144, 48, 95, 15, 48, 15, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 15, 201, 201, 201, 201, 201, 198, 198, 432, 48, 48, 48, 15, 14, 14, 1, 15, 15] 603
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: 1239
number of broken/clashed sets: 269
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071579 none CCC[C@H](O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 7, 12, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [142, 132, 63, 29, 63, 63, 9, 29, 1, 9, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 142, 142, 142, 142, 142, 132, 132, 189, 9, 9, 9, 1, 1, 1, 14, 1, 1] 603
rigid atoms, others: [33, 34, 35, 37, 38, 8, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 836
number of broken/clashed sets: 269
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071579 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071579
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071579/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071579
Building REAL250005071580
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071580'
/scratch/stefan/7916153/working/building/REAL250005071580 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071580

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071580/0 /scratch/stefan/7916153/working/building/REAL250005071580 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 716)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/716
`/scratch/stefan/7916153/working/3D/716' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1(F)CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071580.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071580.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071580/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071580 none CN(C(=O)C1(F)CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 15, 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]
dock color type numbers: [7, 7, 7, 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, 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, 18, 18, 39, 39, 39, 39, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 7, 7, 7, 39, 39, 39, 39, 39, 39, 1, 1, 1, 21, 1, 1] 70
rigid atoms, others: [32, 1, 34, 35, 9, 10, 11, 12, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 141
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071580 none CN(C(=O)C1(F)CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 15, 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]
dock color type numbers: [7, 7, 7, 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, 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: [22, 7, 1, 7, 1, 1, 1, 1, 1, 22, 39, 39, 39, 60, 60, 70, 70, 70, 70, 70, 39, 22, 22, 22, 1, 1, 1, 1, 1, 1, 39, 39, 39, 70, 39, 39] 70
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35])
total number of confs: 214
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071580 none CN(C(=O)C1(F)CCC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 15, 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]
dock color type numbers: [7, 7, 7, 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, 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: [40, 22, 40, 49, 49, 70, 70, 70, 70, 22, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 40, 40, 40, 70, 70, 70, 70, 70, 70, 22, 21, 21, 1, 22, 22] 70
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: 212
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071580 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071580
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071580/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071580
Building REAL250005071581
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071581'
/scratch/stefan/7916153/working/building/REAL250005071581 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071581

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071581/0 /scratch/stefan/7916153/working/building/REAL250005071581 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 717)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/717
`/scratch/stefan/7916153/working/3D/717' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CNC=N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071581.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071581.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071581/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071581 none CN(C(=O)C1=CNC=N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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: [8, 1, 8, 24, 24, 43, 43, 43, 43, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 8, 8, 8, 43, 43, 43, 1, 1, 1, 24, 1, 1] 77
rigid atoms, others: [32, 1, 9, 10, 11, 12, 20, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 124
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071581 none CN(C(=O)C1=CNC=N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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: [25, 8, 1, 8, 1, 1, 1, 1, 1, 25, 43, 43, 43, 67, 67, 77, 77, 77, 77, 77, 43, 25, 25, 25, 1, 1, 1, 43, 43, 43, 77, 43, 43] 77
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32])
total number of confs: 226
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071581 none CN(C(=O)C1=CNC=N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 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]
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: [48, 24, 48, 71, 71, 77, 77, 77, 77, 24, 24, 11, 1, 11, 1, 1, 1, 1, 1, 1, 24, 48, 48, 48, 77, 77, 77, 24, 24, 24, 1, 24, 24] 77
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: 199
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071581 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071581/1 /scratch/stefan/7916153/working/building/REAL250005071581 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 718)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/718
`/scratch/stefan/7916153/working/3D/718' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CN=CN1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071581.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071581.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071581/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071581 none CN(C(=O)C1=CN=CN1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 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]
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: [9, 1, 9, 28, 28, 72, 72, 72, 72, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 9, 9, 9, 72, 72, 72, 1, 1, 1, 22, 1, 1] 114
rigid atoms, others: [32, 1, 9, 10, 11, 12, 20, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30])
total number of confs: 167
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071581 none CN(C(=O)C1=CN=CN1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 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]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [33, 11, 1, 11, 1, 1, 1, 1, 1, 33, 72, 72, 72, 107, 107, 114, 114, 114, 114, 114, 72, 33, 33, 33, 1, 1, 1, 72, 72, 72, 114, 72, 72] 114
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32])
total number of confs: 348
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071581 none CN(C(=O)C1=CN=CN1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 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]
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: [49, 22, 49, 90, 90, 114, 114, 114, 114, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 49, 49, 49, 114, 114, 114, 22, 22, 22, 1, 22, 22] 114
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: 287
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071581 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071581
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071581/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071581/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071581
Building REAL250005071582
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071582'
/scratch/stefan/7916153/working/building/REAL250005071582 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071582

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071582/0 /scratch/stefan/7916153/working/building/REAL250005071582 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 719)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/719
`/scratch/stefan/7916153/working/3D/719' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1CC(=O)C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071582.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071582.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071582/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071582 none CN(C(=O)C1CC(=O)C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 11, 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]
dock color type numbers: [7, 7, 7, 6, 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]
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: [6, 1, 6, 21, 21, 43, 43, 43, 43, 1, 1, 1, 1, 4, 4, 15, 15, 15, 15, 15, 1, 7, 7, 7, 43, 43, 43, 43, 43, 1, 1, 1, 15, 1, 1] 72
rigid atoms, others: [1, 34, 33, 9, 10, 11, 12, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 152
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071582 none CN(C(=O)C1CC(=O)C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 11, 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]
dock color type numbers: [7, 7, 7, 6, 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]
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, 6, 1, 6, 1, 1, 1, 1, 1, 21, 43, 43, 43, 62, 62, 72, 72, 72, 72, 72, 43, 21, 21, 21, 1, 1, 1, 1, 1, 43, 43, 43, 72, 43, 43] 72
rigid atoms, others: [2, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34])
total number of confs: 216
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071582 none CN(C(=O)C1CC(=O)C1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 11, 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]
dock color type numbers: [7, 7, 7, 6, 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]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [35, 16, 35, 53, 53, 72, 72, 72, 72, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 35, 35, 35, 72, 72, 72, 72, 72, 16, 15, 15, 1, 15, 15] 72
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: 219
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071582 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071582
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071582/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071582
Building REAL250005071583
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071583'
/scratch/stefan/7916153/working/building/REAL250005071583 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071583

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071583/0 /scratch/stefan/7916153/working/building/REAL250005071583 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 720)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/720
`/scratch/stefan/7916153/working/3D/720' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1(O)COC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071583.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071583.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071583/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071583 none CN(C(=O)C1(O)COC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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']
dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 4, 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]
1  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 19, 19, 26, 26, 26, 26, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 9, 9, 9, 78, 26, 26, 26, 26, 1, 1, 1, 17, 1, 1] 159
rigid atoms, others: [1, 34, 33, 9, 10, 11, 12, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32])
total number of confs: 177
number of broken/clashed sets: 53
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071583 none CN(C(=O)C1(O)COC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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']
dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 4, 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]
1  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [12, 6, 1, 6, 1, 1, 1, 1, 1, 12, 26, 26, 26, 46, 46, 53, 53, 53, 53, 53, 26, 12, 12, 12, 6, 1, 1, 1, 1, 26, 26, 26, 53, 26, 26] 159
rigid atoms, others: [2, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34])
total number of confs: 161
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071583 none CN(C(=O)C1(O)COC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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']
dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 12, 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]
dock color type numbers: [7, 7, 7, 6, 7, 4, 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]
1  hydrogens need rotated
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [37, 18, 37, 48, 48, 53, 53, 53, 53, 18, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 37, 37, 37, 159, 53, 53, 53, 53, 18, 17, 17, 1, 18, 18] 159
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: 304
number of broken/clashed sets: 53
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071583 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071583
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071583/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071583
Building REAL250005071584
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071584'
/scratch/stefan/7916153/working/building/REAL250005071584 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071584

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071584/0 /scratch/stefan/7916153/working/building/REAL250005071584 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 721)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/721
`/scratch/stefan/7916153/working/3D/721' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)=C1CC1)

`REAL250005071584.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071584.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071584/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071584 none CC(C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)=C1CC1 NO_LONG_NAME
dock atom types: ['C.3', '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.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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, 99, 71, 99, 25, 71, 25, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 128, 128, 128, 128, 128, 128, 71, 71, 71, 25, 24, 24, 1, 24, 24, 128, 128, 128, 128] 128
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])
total number of confs: 382
number of broken/clashed sets: 52
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071584 none CC(C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)=C1CC1 NO_LONG_NAME
dock atom types: ['C.3', '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.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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: [50, 26, 9, 26, 1, 9, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 50, 50, 50, 50, 50, 50, 9, 9, 9, 1, 1, 1, 24, 1, 1, 50, 50, 50, 50] 128
rigid atoms, others: [32, 4, 6, 7, 8, 9, 17, 27, 28, 29, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 33, 34, 35, 36])
total number of confs: 188
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071584 none CC(C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)=C1CC1 NO_LONG_NAME
dock atom types: ['C.3', '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.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 6, 7, 7, 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: [1, 1, 1, 7, 7, 20, 20, 50, 50, 50, 108, 108, 128, 128, 128, 128, 128, 50, 1, 1, 1, 2, 2, 2, 20, 20, 20, 50, 50, 50, 128, 50, 50, 1, 1, 1, 1] 128
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: 364
number of broken/clashed sets: 52
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071584 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071584
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071584/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071584
Building REAL250005071585
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071585'
/scratch/stefan/7916153/working/building/REAL250005071585 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071585

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071585/0 /scratch/stefan/7916153/working/building/REAL250005071585 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 722)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/722
`/scratch/stefan/7916153/working/3D/722' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071585.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071585.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071585/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071585 none CC1=CC1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [66, 66, 66, 28, 9, 28, 1, 9, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 66, 66, 66, 66, 66, 9, 9, 9, 1, 1, 1, 23, 1, 1] 139
rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 215
number of broken/clashed sets: 61
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071585 none CC1=CC1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 31, 31, 66, 66, 66, 119, 119, 139, 139, 139, 139, 139, 66, 2, 2, 2, 1, 1, 31, 31, 31, 66, 66, 66, 139, 66, 66] 139
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: 395
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071585 none CC1=CC1C(=O)N(C)C1CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 98, 70, 98, 23, 70, 23, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 139, 139, 139, 139, 139, 70, 70, 70, 23, 22, 23, 1, 23, 23] 139
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: 421
number of broken/clashed sets: 61
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071585 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071585
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071585/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071585
Building REAL250005071586
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071586'
/scratch/stefan/7916153/working/building/REAL250005071586 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071586

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071586/0 /scratch/stefan/7916153/working/building/REAL250005071586 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 723)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/723
`/scratch/stefan/7916153/working/3D/723' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C(=O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071586.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071586.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071586/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071586 none CN(C)C(=O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 5, 1, 11, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [106, 106, 106, 91, 106, 67, 91, 24, 67, 24, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 106, 106, 106, 106, 106, 106, 67, 67, 67, 24, 23, 23, 1, 24, 24] 106
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: 296
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071586 none CN(C)C(=O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 5, 1, 11, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [47, 44, 49, 28, 46, 9, 28, 1, 9, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 49, 49, 49, 49, 49, 49, 9, 9, 9, 1, 1, 1, 23, 1, 1] 106
rigid atoms, others: [32, 34, 35, 7, 9, 10, 11, 12, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33])
total number of confs: 186
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071586 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071586
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071586/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071586
Building REAL250005071587
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071587'
/scratch/stefan/7916153/working/building/REAL250005071587 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071587

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071587/0 /scratch/stefan/7916153/working/building/REAL250005071587 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 724)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/724
`/scratch/stefan/7916153/working/3D/724' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071587.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071587.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071587/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071587 none CCCC(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 197, 144, 96, 144, 47, 96, 15, 47, 15, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 197, 197, 144, 432, 47, 47, 47, 15, 14, 14, 1, 14, 14] 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: 1243
number of broken/clashed sets: 269
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071587 none CCCC(O)C(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 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, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [143, 133, 63, 29, 63, 9, 29, 1, 9, 1, 1, 1, 1, 6, 6, 14, 14, 15, 14, 14, 1, 143, 143, 143, 143, 143, 133, 133, 63, 189, 9, 9, 9, 1, 1, 1, 14, 1, 1] 603
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 841
number of broken/clashed sets: 269
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071587 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071587
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071587/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071587
Building REAL250005071588
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071588'
/scratch/stefan/7916153/working/building/REAL250005071588 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071588

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071588/0 /scratch/stefan/7916153/working/building/REAL250005071588 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 725)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/725
`/scratch/stefan/7916153/working/3D/725' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(O)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071588.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071588.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071588/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071588 none CCC(O)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens 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, 195, 168, 195, 88, 51, 88, 17, 51, 17, 16, 5, 1, 5, 1, 1, 1, 1, 1, 1, 17, 201, 201, 201, 201, 201, 195, 585, 168, 168, 51, 51, 51, 17, 16, 17, 1, 17, 17] 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: 1374
number of broken/clashed sets: 273
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071588 none CCC(O)CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [141, 119, 82, 119, 25, 9, 25, 1, 9, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 141, 141, 141, 141, 141, 119, 357, 82, 82, 9, 9, 9, 1, 1, 1, 17, 1, 1] 603
rigid atoms, others: [33, 34, 35, 37, 38, 7, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36])
total number of confs: 989
number of broken/clashed sets: 273
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071588 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071588
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071588/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071588
Building REAL250005071589
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071589'
/scratch/stefan/7916153/working/building/REAL250005071589 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071589

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071589/0 /scratch/stefan/7916153/working/building/REAL250005071589 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 726)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/726
`/scratch/stefan/7916153/working/3D/726' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)CCCCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071589.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071589.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071589/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071589 none CN(C(=O)CCCCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 15, 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, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 10, 29, 53, 53, 145, 170, 200, 200, 10, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 29, 29, 29, 145, 145, 182, 182, 201, 200, 201, 201, 10, 9, 10, 1, 10, 10] 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: 905
number of broken/clashed sets: 72
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071589 none CN(C(=O)CCCCF)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 15, 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, 7]
dock color type numbers: [7, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 22, 22, 83, 104, 127, 163, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 1, 9, 9, 9, 83, 83, 113, 113, 128, 127, 164, 164, 1, 1, 1, 10, 1, 1] 201
rigid atoms, others: [32, 1, 34, 36, 37, 33, 9, 10, 11, 12, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35])
total number of confs: 813
number of broken/clashed sets: 72
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071589 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071589
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071589/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071589
Building REAL250005071590
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071590'
/scratch/stefan/7916153/working/building/REAL250005071590 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071590

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071590/0 /scratch/stefan/7916153/working/building/REAL250005071590 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 727)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/727
`/scratch/stefan/7916153/working/3D/727' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)[C@H]1CC(=O)N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071590.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071590.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071590/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071590 none CN(C(=O)[C@H]1CC(=O)N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 6, 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]
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, 20, 20, 47, 47, 47, 47, 47, 1, 1, 1, 1, 5, 5, 18, 18, 18, 18, 18, 1, 8, 8, 8, 47, 47, 47, 1, 1, 1, 18, 1, 1] 93
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 21, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 165
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071590 none CN(C(=O)[C@H]1CC(=O)N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 6, 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]
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: [24, 7, 1, 7, 1, 1, 1, 1, 1, 1, 24, 47, 47, 47, 79, 79, 93, 93, 93, 93, 93, 47, 24, 24, 24, 1, 1, 1, 47, 47, 47, 93, 47, 47] 93
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33])
total number of confs: 279
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071590 none CN(C(=O)[C@H]1CC(=O)N1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 6, 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]
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: [45, 18, 45, 66, 66, 93, 93, 93, 93, 93, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 45, 45, 45, 93, 93, 93, 18, 18, 18, 1, 18, 18] 93
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: 275
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071590 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071590
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071590/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071590
Building REAL250005071591
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071591'
/scratch/stefan/7916153/working/building/REAL250005071591 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071591

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071591/0 /scratch/stefan/7916153/working/building/REAL250005071591 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 728)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/728
`/scratch/stefan/7916153/working/3D/728' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1)

`REAL250005071591.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071591.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071591/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071591 none COC1(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1 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', '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, 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, 7, 6, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [37, 36, 21, 8, 21, 1, 8, 1, 1, 1, 1, 4, 4, 17, 17, 17, 17, 17, 1, 36, 36, 37, 37, 37, 9, 9, 9, 1, 1, 1, 17, 1, 1, 36, 36, 36, 36] 67
rigid atoms, others: [32, 5, 7, 8, 9, 10, 18, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 30, 33, 34, 35, 36])
total number of confs: 138
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071591 none COC1(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1 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', '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, 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, 7, 6, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 6, 6, 16, 16, 36, 36, 36, 60, 60, 67, 67, 67, 67, 67, 36, 1, 1, 4, 4, 4, 16, 16, 16, 36, 36, 36, 67, 36, 36, 1, 1, 1, 1] 67
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: 209
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071591 none COC1(C(=O)N(C)C2CN(C(=O)C3=CC(=O)[N-]O3)C2)CC1 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', '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, 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, 7, 6, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 48, 34, 48, 17, 34, 17, 17, 10, 1, 10, 1, 1, 1, 1, 1, 1, 17, 67, 67, 67, 67, 67, 34, 34, 34, 17, 17, 17, 1, 17, 17, 67, 67, 67, 67] 67
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: 203
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071591 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071591
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071591/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071591
Building REAL250005071592
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071592'
/scratch/stefan/7916153/working/building/REAL250005071592 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071592

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071592/0 /scratch/stefan/7916153/working/building/REAL250005071592 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 729)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/729
`/scratch/stefan/7916153/working/3D/729' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1CSC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071592.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071592.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071592/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071592 none CN(C(=O)C1CSC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 14, 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]
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]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 26, 26, 57, 57, 57, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 9, 9, 9, 57, 57, 57, 57, 57, 1, 1, 1, 27, 1, 1] 123
rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 19, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 31])
total number of confs: 196
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071592 none CN(C(=O)C1CSC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 14, 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]
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]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [22, 7, 1, 7, 1, 1, 1, 1, 22, 57, 57, 57, 110, 110, 123, 123, 123, 123, 123, 57, 22, 22, 22, 1, 1, 1, 1, 1, 57, 57, 57, 123, 57, 57] 123
rigid atoms, others: [2, 4, 5, 6, 7, 23, 24, 25, 26, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33])
total number of confs: 350
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071592 none CN(C(=O)C1CSC1)C1CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 14, 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]
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]
0  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [82, 27, 82, 105, 105, 123, 123, 123, 27, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 27, 82, 82, 82, 123, 123, 123, 123, 123, 27, 26, 27, 1, 27, 27] 123
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: 352
number of broken/clashed sets: 50
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071592 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071592
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071592/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071592
Building REAL250005071593
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071593'
/scratch/stefan/7916153/working/building/REAL250005071593 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071593

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071593/0 /scratch/stefan/7916153/working/building/REAL250005071593 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 730)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/730
`/scratch/stefan/7916153/working/3D/730' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N(C)C1CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071593.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071593.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071593/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071593 none C=CC(=O)N(C)C1CN(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', 'N.am', 'C.2', 'O.2', 'C.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [82, 82, 63, 82, 24, 63, 24, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 82, 82, 82, 63, 63, 63, 24, 23, 24, 1, 24, 24] 82
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])
total number of confs: 215
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071593 none C=CC(=O)N(C)C1CN(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', 'N.am', 'C.2', 'O.2', 'C.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [58, 24, 9, 24, 1, 9, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 58, 58, 58, 9, 9, 9, 1, 1, 1, 24, 1, 1] 82
rigid atoms, others: [4, 6, 7, 8, 9, 17, 24, 25, 26, 28, 29] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 27])
total number of confs: 196
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071593 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071593
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071593/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071593
Building REAL250005071594
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071594'
/scratch/stefan/7916153/working/building/REAL250005071594 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071594

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071594/0 /scratch/stefan/7916153/working/building/REAL250005071594 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 731)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/731
`/scratch/stefan/7916153/working/3D/731' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC(=O)N2)C1)

`REAL250005071594.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071594.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071594/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071594 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 22, 22, 52, 52, 52, 52, 52, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 1, 9, 9, 9, 52, 1, 1, 1, 29, 29, 29, 29, 1, 1] 164
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31])
total number of confs: 175
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071594 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 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: [33, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 52, 52, 52, 75, 75, 164, 164, 164, 164, 52, 33, 33, 33, 1, 52, 52, 52, 164, 164, 164, 164, 52, 52] 164
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 493
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071594 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 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: [94, 29, 94, 142, 142, 164, 164, 164, 164, 164, 29, 29, 11, 1, 11, 1, 1, 1, 1, 1, 29, 94, 94, 94, 164, 29, 29, 29, 1, 1, 1, 1, 29, 29] 164
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 421
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071594 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071594
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071594/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071594
Building REAL250005071595
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071595'
/scratch/stefan/7916153/working/building/REAL250005071595 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071595

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071595/0 /scratch/stefan/7916153/working/building/REAL250005071595 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 732)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/732
`/scratch/stefan/7916153/working/3D/732' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC(F)C2)C1)

`REAL250005071595.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071595.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071595/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071595 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC(F)C2)C1 NO_LONG_NAME
dock atom types: ['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.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', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 22, 22, 62, 62, 62, 62, 62, 1, 1, 1, 1, 6, 6, 33, 33, 33, 33, 1, 9, 9, 9, 62, 1, 1, 1, 33, 33, 33, 33, 33, 33, 1, 1] 180
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 20, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33])
total number of confs: 191
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071595 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC(F)C2)C1 NO_LONG_NAME
dock atom types: ['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.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', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [37, 10, 1, 10, 1, 1, 1, 1, 1, 1, 37, 62, 62, 62, 87, 87, 180, 180, 180, 180, 62, 37, 37, 37, 1, 62, 62, 62, 180, 180, 180, 180, 180, 180, 62, 62] 180
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 561
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071595 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2CC(F)C2)C1 NO_LONG_NAME
dock atom types: ['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.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', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 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: [7, 7, 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
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [95, 33, 95, 145, 145, 180, 180, 180, 180, 180, 33, 33, 8, 1, 8, 1, 1, 1, 1, 1, 33, 95, 95, 95, 180, 33, 33, 33, 1, 1, 1, 1, 1, 1, 33, 33] 180
rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35])
total number of confs: 435
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071595 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071595
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071595/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071595
Building REAL250005071596
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071596'
/scratch/stefan/7916153/working/building/REAL250005071596 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071596

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071596/0 /scratch/stefan/7916153/working/building/REAL250005071596 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 733)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/733
`/scratch/stefan/7916153/working/3D/733' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CC=NO2)C1)

`REAL250005071596.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071596.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071596/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071596 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CC=NO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 21, 21, 43, 43, 43, 43, 43, 1, 1, 1, 1, 5, 5, 24, 24, 24, 24, 1, 9, 9, 9, 43, 1, 1, 1, 24, 24, 1, 1] 95
rigid atoms, others: [1, 10, 11, 12, 13, 20, 25, 26, 27, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29])
total number of confs: 121
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071596 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CC=NO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 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: [23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 43, 43, 43, 63, 63, 95, 95, 95, 95, 43, 23, 23, 23, 1, 43, 43, 43, 95, 95, 43, 43] 95
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 256
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071596 none CN(C(=O)C1=CC(=O)[N-]O1)C1CN(C(=O)C2=CC=NO2)C1 NO_LONG_NAME
dock atom types: ['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.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 1, 1, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [54, 25, 54, 82, 82, 95, 95, 95, 95, 95, 25, 24, 9, 1, 9, 1, 1, 1, 1, 1, 25, 54, 54, 54, 95, 25, 24, 24, 1, 1, 25, 25] 95
rigid atoms, others: [13, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 238
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071596 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071596
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071596/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071596
Building REAL250005071597
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071597'
/scratch/stefan/7916153/working/building/REAL250005071597 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071597

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071597/0 /scratch/stefan/7916153/working/building/REAL250005071597 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 734)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/734
`/scratch/stefan/7916153/working/3D/734' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC[C@@H]1C[C@H]2CC[C@@H](C1)N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005071597.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071597.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071597/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071597 none CC(=O)NC[C@@H]1C[C@H]2CC[C@@H](C1)N2C(=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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 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]
dock color type numbers: [7, 7, 6, 4, 7, 7, 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
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [119, 119, 119, 98, 32, 32, 32, 32, 31, 31, 32, 32, 32, 32, 32, 9, 1, 9, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 98, 98, 32, 32, 32, 32, 32, 32, 32, 32, 1] 119
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: 394
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071597 none CC(=O)NC[C@@H]1C[C@H]2CC[C@@H](C1)N2C(=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', '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, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 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]
dock color type numbers: [7, 7, 6, 4, 7, 7, 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
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 31, 31, 31, 31, 31, 48, 48, 48, 48, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 32] 119
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 36, 37, 30, 31] set([0, 1, 2, 3, 38, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 168
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071597 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071597
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071597/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071597
Building REAL250005071598
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071598'
/scratch/stefan/7916153/working/building/REAL250005071598 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071598

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071598/0 /scratch/stefan/7916153/working/building/REAL250005071598 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 735)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/735
`/scratch/stefan/7916153/working/3D/735' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1[C@@H]2CC[C@H]1C[C@H](CNC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005071598.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071598.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071598/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071598 none CC(=O)N1[C@@H]2CC[C@H]1C[C@H](CNC(=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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 7, 5, 5, 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, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 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, 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, 51, 57, 51, 51, 51, 51, 51, 51, 51, 51, 24, 51, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 51, 57, 57, 57, 51, 51, 51, 51, 51, 51, 24, 24, 7, 1, 51, 51] 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: 186
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071598 none CC(=O)N1[C@@H]2CC[C@H]1C[C@H](CNC(=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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 7, 5, 5, 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, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 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, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 47, 47, 47, 51, 51, 51, 51, 51, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 47, 51, 1, 1] 57
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 38, 37, 23, 27, 28, 29, 30, 31] set([0, 33, 2, 35, 36, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26])
total number of confs: 135
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071598 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071598
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071598/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071598
Building REAL250005071599
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071599'
/scratch/stefan/7916153/working/building/REAL250005071599 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071599

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071599/0 /scratch/stefan/7916153/working/building/REAL250005071599 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 736)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/736
`/scratch/stefan/7916153/working/3D/736' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071599.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071599.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071599/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071599 none CCC(=O)NCC(C)CN(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', '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, 5, 1, 11, 8, 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]
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]
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, 120, 120, 120, 86, 46, 36, 46, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 170, 170, 170, 170, 170, 120, 86, 86, 46, 46, 46, 46, 36, 36, 13, 13, 13, 1] 170
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])
total number of confs: 792
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071599 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071599
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071599/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071599
Building REAL250005071600
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071600'
/scratch/stefan/7916153/working/building/REAL250005071600 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071600

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071600/0 /scratch/stefan/7916153/working/building/REAL250005071600 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 737)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/737
`/scratch/stefan/7916153/working/3D/737' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071600.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071600.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071600/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071600 none COCCC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 184, 84, 84, 84, 59, 28, 22, 28, 13, 8, 13, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 184, 184, 84, 59, 59, 28, 28, 28, 28, 22, 22, 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: 888
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071600 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071600
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071600/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071600
Building REAL250005071601
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071601'
/scratch/stefan/7916153/working/building/REAL250005071601 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071601

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071601/0 /scratch/stefan/7916153/working/building/REAL250005071601 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 738)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/738
`/scratch/stefan/7916153/working/3D/738' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071601.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071601.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071601/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071601 none CC(=O)NCC(C)CN(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', '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']
dock atom type numbers: [5, 1, 11, 8, 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]
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]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 48, 33, 27, 33, 12, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 48, 48, 33, 33, 33, 33, 27, 27, 12, 12, 12, 1] 51
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])
total number of confs: 229
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071601 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071601
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071601/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071601
Building REAL250005071602
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071602'
/scratch/stefan/7916153/working/building/REAL250005071602 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071602

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071602/0 /scratch/stefan/7916153/working/building/REAL250005071602 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 739)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/739
`/scratch/stefan/7916153/working/3D/739' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1CC1)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071602.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071602.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071602/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071602 none CC(CNC(=O)C1CC1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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: [43, 32, 43, 81, 104, 104, 104, 171, 171, 12, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 81, 81, 104, 171, 171, 171, 171, 171, 32, 32, 12, 12, 12, 1] 171
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: 679
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071602 none CC(CNC(=O)C1CC1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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: [65, 35, 11, 11, 1, 11, 1, 1, 1, 68, 109, 129, 129, 166, 166, 171, 171, 171, 171, 171, 69, 69, 69, 69, 35, 35, 11, 1, 1, 1, 1, 1, 108, 109, 129, 129, 129, 171] 171
rigid atoms, others: [4, 6, 7, 8, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37])
total number of confs: 720
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071602 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071602
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071602/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071602
Building REAL250005071603
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071603'
/scratch/stefan/7916153/working/building/REAL250005071603 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071603

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071603/0 /scratch/stefan/7916153/working/building/REAL250005071603 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 740)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/740
`/scratch/stefan/7916153/working/3D/740' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1CCC1)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071603.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071603.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071603/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071603 none CC(CNC(=O)C1CCC1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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: [44, 32, 44, 82, 110, 110, 110, 201, 201, 201, 12, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 82, 82, 110, 201, 201, 201, 201, 201, 201, 201, 32, 32, 12, 12, 12, 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: 759
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071603 none CC(CNC(=O)C1CCC1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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: [71, 41, 10, 10, 1, 10, 1, 1, 1, 1, 75, 124, 147, 147, 195, 195, 201, 201, 201, 201, 201, 75, 75, 75, 75, 41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 124, 124, 147, 147, 147, 201] 201
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40])
total number of confs: 828
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071603 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071603
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071603/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071603
Building REAL250005071604
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071604'
/scratch/stefan/7916153/working/building/REAL250005071604 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071604

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071604/0 /scratch/stefan/7916153/working/building/REAL250005071604 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 741)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/741
`/scratch/stefan/7916153/working/3D/741' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)CC1CC1)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071604.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071604.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071604/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071604 none CC(CNC(=O)CC1CC1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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: [42, 31, 42, 76, 90, 90, 90, 157, 201, 201, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 76, 76, 90, 157, 157, 201, 201, 201, 201, 201, 31, 31, 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: 898
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071604 none CC(CNC(=O)CC1CC1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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: [61, 35, 20, 20, 3, 20, 1, 1, 1, 1, 61, 120, 140, 140, 195, 195, 201, 201, 201, 201, 201, 61, 61, 61, 61, 35, 35, 20, 3, 3, 1, 1, 1, 1, 1, 120, 120, 140, 140, 140, 201] 201
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40])
total number of confs: 807
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071604 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071604
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071604/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071604
Building REAL250005071605
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071605'
/scratch/stefan/7916153/working/building/REAL250005071605 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071605

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071605/0 /scratch/stefan/7916153/working/building/REAL250005071605 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 742)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/742
`/scratch/stefan/7916153/working/3D/742' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071605.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071605.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071605/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071605 none COCC(=O)NCC(C)CN(C)C(=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', '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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 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]
dock color type numbers: [7, 3, 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]
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, 77, 39, 39, 39, 29, 19, 17, 19, 14, 8, 14, 1, 8, 1, 1, 1, 1, 1, 1, 81, 81, 81, 77, 77, 39, 29, 29, 19, 19, 19, 19, 17, 17, 14, 14, 14, 1] 81
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: 345
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071605 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071605
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071605/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071605
Building REAL250005071606
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071606'
/scratch/stefan/7916153/working/building/REAL250005071606 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071606

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071606/0 /scratch/stefan/7916153/working/building/REAL250005071606 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 743)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/743
`/scratch/stefan/7916153/working/3D/743' -> `0.mol2'
Preparing input files

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

`REAL250005071606.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071606.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071606/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071606 none CCCC(=O)NCC(C)CN(C)C(=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', '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, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 114, 114, 91, 51, 36, 51, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 114, 91, 91, 51, 51, 51, 51, 36, 36, 14, 14, 14, 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: 929
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071606 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071606
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071606/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071606
Building REAL250005071607
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071607'
/scratch/stefan/7916153/working/building/REAL250005071607 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071607

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071607/0 /scratch/stefan/7916153/working/building/REAL250005071607 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 744)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/744
`/scratch/stefan/7916153/working/3D/744' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071607.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071607.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071607/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071607 none CC(C)CC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [152, 156, 156, 114, 114, 114, 82, 42, 32, 42, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 156, 156, 156, 156, 114, 82, 82, 42, 42, 42, 42, 32, 32, 13, 13, 13, 1] 156
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: 763
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071607 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071607
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071607/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071607
Building REAL250005071608
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071608'
/scratch/stefan/7916153/working/building/REAL250005071608 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071608

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071608/0 /scratch/stefan/7916153/working/building/REAL250005071608 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 745)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/745
`/scratch/stefan/7916153/working/3D/745' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1CC1C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071608.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071608.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071608/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071608 none CC(CNC(=O)C1CC1C)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [48, 35, 48, 87, 122, 122, 122, 191, 191, 191, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 87, 87, 122, 191, 191, 191, 191, 191, 191, 191, 35, 35, 13, 13, 13, 1] 191
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: 734
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071608 none CC(CNC(=O)C1CC1C)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [69, 35, 11, 11, 1, 11, 1, 1, 1, 1, 71, 116, 135, 135, 184, 184, 191, 191, 191, 191, 191, 73, 73, 73, 73, 35, 35, 11, 1, 1, 1, 1, 2, 2, 2, 115, 116, 135, 135, 135, 191] 191
rigid atoms, others: [4, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 803
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071608 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071608
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071608/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071608
Building REAL250005071609
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071609'
/scratch/stefan/7916153/working/building/REAL250005071609 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071609

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071609/0 /scratch/stefan/7916153/working/building/REAL250005071609 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 746)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/746
`/scratch/stefan/7916153/working/3D/746' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071609.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071609.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071609/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071609 none CCOCC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 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
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [123, 120, 110, 37, 37, 37, 27, 18, 17, 18, 14, 8, 14, 1, 8, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 110, 110, 37, 27, 27, 18, 18, 18, 18, 17, 17, 14, 14, 14, 1] 123
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: 489
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071609 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071609
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071609/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071609
Building REAL250005071610
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071610'
/scratch/stefan/7916153/working/building/REAL250005071610 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071610

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071610/0 /scratch/stefan/7916153/working/building/REAL250005071610 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 747)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/747
`/scratch/stefan/7916153/working/3D/747' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071610.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071610.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071610/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071610 none CC(C)=CC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
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, 104, 104, 104, 75, 39, 30, 39, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 135, 135, 104, 75, 75, 39, 39, 39, 39, 30, 30, 13, 13, 13, 1] 135
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: 562
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071610 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071610
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071610/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071610
Building REAL250005071611
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071611'
/scratch/stefan/7916153/working/building/REAL250005071611 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071611

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071611/0 /scratch/stefan/7916153/working/building/REAL250005071611 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 748)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/748
`/scratch/stefan/7916153/working/3D/748' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071611.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071611.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071611/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071611 none CCCCC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 198, 78, 78, 78, 65, 35, 27, 35, 12, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 198, 198, 78, 65, 65, 35, 35, 35, 35, 27, 27, 12, 12, 12, 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: 854
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071611 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071611
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071611/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071611
Building REAL250005071612
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071612'
/scratch/stefan/7916153/working/building/REAL250005071612 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071612

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071612/0 /scratch/stefan/7916153/working/building/REAL250005071612 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 749)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/749
`/scratch/stefan/7916153/working/3D/749' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071612.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071612.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071612/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071612 none CC(C)C(=O)NCC(C)CN(C)C(=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', '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, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 148, 201, 148, 148, 110, 56, 39, 56, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 148, 110, 110, 56, 56, 56, 56, 39, 39, 14, 14, 14, 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: 921
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071612 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071612
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071612/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071612
Building REAL250005071613
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071613'
/scratch/stefan/7916153/working/building/REAL250005071613 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071613

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071613/0 /scratch/stefan/7916153/working/building/REAL250005071613 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 750)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/750
`/scratch/stefan/7916153/working/3D/750' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071613.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071613.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071613/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071613 none CCC(C)C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.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, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [158, 154, 112, 154, 112, 112, 80, 44, 31, 44, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 158, 154, 154, 154, 154, 112, 80, 80, 44, 44, 44, 44, 31, 31, 13, 13, 13, 1] 158
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: 730
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071613 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071613
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071613/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071613
Building REAL250005071614
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071614'
/scratch/stefan/7916153/working/building/REAL250005071614 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071614

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071614/0 /scratch/stefan/7916153/working/building/REAL250005071614 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 751)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/751
`/scratch/stefan/7916153/working/3D/751' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071614.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071614.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071614/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071614 none COC(C)C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [60, 58, 34, 58, 34, 34, 26, 18, 16, 18, 13, 8, 13, 1, 8, 1, 1, 1, 1, 1, 1, 60, 60, 60, 58, 58, 58, 58, 34, 26, 26, 18, 18, 18, 18, 16, 16, 13, 13, 13, 1] 60
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: 256
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071614 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071614
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071614/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071614
Building REAL250005071615
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071615'
/scratch/stefan/7916153/working/building/REAL250005071615 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071615

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071615/0 /scratch/stefan/7916153/working/building/REAL250005071615 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 752)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/752
`/scratch/stefan/7916153/working/3D/752' -> `0.mol2'
Preparing input files

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

`REAL250005071615.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071615.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071615/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071615 none C=CCCC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 190, 76, 76, 76, 51, 26, 22, 26, 13, 7, 13, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 190, 190, 76, 51, 51, 26, 26, 26, 26, 22, 22, 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: 851
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071615 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071615
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071615/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071615
Building REAL250005071616
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071616'
/scratch/stefan/7916153/working/building/REAL250005071616 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071616

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071616/0 /scratch/stefan/7916153/working/building/REAL250005071616 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 753)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/753
`/scratch/stefan/7916153/working/3D/753' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(C)C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071616.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071616.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071616/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071616 none CC=C(C)C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [153, 153, 117, 153, 117, 117, 89, 45, 34, 45, 12, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 153, 153, 153, 117, 89, 89, 45, 45, 45, 45, 34, 34, 12, 12, 12, 1] 153
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: 621
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071616 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071616
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071616/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071616
Building REAL250005071617
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071617'
/scratch/stefan/7916153/working/building/REAL250005071617 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071617

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071617/0 /scratch/stefan/7916153/working/building/REAL250005071617 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 754)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/754
`/scratch/stefan/7916153/working/3D/754' -> `0.mol2'
Preparing input files

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

`REAL250005071617.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071617.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071617/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071617 none CC(CNC(=O)C1(C)CC1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [28, 21, 28, 45, 63, 63, 63, 97, 97, 97, 10, 6, 10, 1, 6, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 45, 45, 63, 97, 97, 97, 97, 97, 97, 97, 21, 21, 10, 10, 10, 1] 97
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: 401
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071617 none CC(CNC(=O)C1(C)CC1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [43, 19, 6, 6, 1, 6, 1, 1, 1, 1, 45, 62, 75, 75, 94, 94, 97, 97, 97, 97, 97, 45, 45, 45, 45, 19, 19, 6, 2, 2, 2, 1, 1, 1, 1, 62, 62, 75, 75, 75, 97] 97
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 403
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071617 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071617
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071617/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071617
Building REAL250005071618
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071618'
/scratch/stefan/7916153/working/building/REAL250005071618 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071618

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071618/0 /scratch/stefan/7916153/working/building/REAL250005071618 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 755)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/755
`/scratch/stefan/7916153/working/3D/755' -> `0.mol2'
Preparing input files

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

`REAL250005071618.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071618.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071618/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071618 none CC(CNC(=O)[C@@H]1C[C@H]1C)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
189  conformations in input
total number of sets (complete confs): 189
using faster count positions algorithm for large data
unique positions, atoms: [44, 32, 44, 84, 112, 112, 112, 189, 189, 189, 189, 189, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 84, 84, 112, 189, 189, 189, 189, 189, 32, 32, 13, 13, 13, 1] 189
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: 742
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071618 none CC(CNC(=O)[C@@H]1C[C@H]1C)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
189  conformations in input
total number of sets (complete confs): 189
using faster count positions algorithm for large data
unique positions, atoms: [68, 35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 71, 116, 138, 138, 177, 177, 189, 189, 189, 189, 189, 72, 72, 72, 72, 35, 35, 11, 1, 1, 2, 2, 2, 115, 116, 138, 138, 138, 189] 189
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 777
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071618 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071618
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071618/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071618
Building REAL250005071619
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071619'
/scratch/stefan/7916153/working/building/REAL250005071619 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071619

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071619/0 /scratch/stefan/7916153/working/building/REAL250005071619 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 756)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/756
`/scratch/stefan/7916153/working/3D/756' -> `0.mol2'
Preparing input files

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

`REAL250005071619.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071619.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071619/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071619 none CC(CNC(=O)[C@H]1C[C@@H]1C)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [49, 35, 49, 88, 122, 122, 122, 191, 191, 191, 191, 191, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 88, 88, 122, 191, 191, 191, 191, 191, 35, 35, 13, 13, 13, 1] 191
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: 741
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071619 none CC(CNC(=O)[C@H]1C[C@@H]1C)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
191  conformations in input
total number of sets (complete confs): 191
using faster count positions algorithm for large data
unique positions, atoms: [67, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 70, 116, 135, 135, 184, 184, 191, 191, 191, 191, 191, 71, 71, 71, 71, 34, 34, 11, 1, 1, 2, 2, 2, 116, 115, 135, 135, 135, 191] 191
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 803
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071619 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071619
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071619/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071619
Building REAL250005071620
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071620'
/scratch/stefan/7916153/working/building/REAL250005071620 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071620

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071620/0 /scratch/stefan/7916153/working/building/REAL250005071620 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 757)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/757
`/scratch/stefan/7916153/working/3D/757' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C(N)=O)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071620.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071620.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071620/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071620 none CC(CNC(=O)C(N)=O)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 8, 11, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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, 7, 7]
0  hydrogens 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, 57, 79, 145, 201, 201, 201, 201, 201, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 145, 145, 201, 201, 201, 57, 57, 20, 20, 20, 1] 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])
total number of confs: 826
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071620 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071620
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071620/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071620
Building REAL250005071621
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071621'
/scratch/stefan/7916153/working/building/REAL250005071621 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071621

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071621/0 /scratch/stefan/7916153/working/building/REAL250005071621 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 758)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/758
`/scratch/stefan/7916153/working/3D/758' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C(C)(C)C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071621.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071621.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071621/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071621 none CC(CNC(=O)C(C)(C)C)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [31, 24, 31, 45, 55, 55, 55, 55, 55, 55, 11, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 45, 45, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 24, 24, 11, 11, 11, 1] 55
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: 244
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071621 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071621
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071621/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071621
Building REAL250005071622
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071622'
/scratch/stefan/7916153/working/building/REAL250005071622 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071622

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071622/0 /scratch/stefan/7916153/working/building/REAL250005071622 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 759)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/759
`/scratch/stefan/7916153/working/3D/759' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071622.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071622.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071622/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071622 none C=CCC(=O)NCC(C)CN(C)C(=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', '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']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 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]
dock color type numbers: [7, 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]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 17, 17, 17, 14, 12, 10, 12, 9, 6, 9, 1, 6, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 17, 14, 14, 12, 12, 12, 12, 10, 10, 9, 9, 9, 1] 35
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: 158
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071622 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071622
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071622/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071622
Building REAL250005071623
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071623'
/scratch/stefan/7916153/working/building/REAL250005071623 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071623

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071623/0 /scratch/stefan/7916153/working/building/REAL250005071623 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 760)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/760
`/scratch/stefan/7916153/working/3D/760' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C[NH+](C)C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071623.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071623.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071623/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071623 none CC(CNC(=O)C[NH+](C)C)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 1, 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
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [5, 4, 5, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 1] 6
rigid atoms, others: [42, 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, 40, 41])
total number of confs: 21
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071623 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071623/1 /scratch/stefan/7916153/working/building/REAL250005071623 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 761)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/761
`/scratch/stefan/7916153/working/3D/761' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)CN(C)C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071623.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071623.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071623/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.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: REAL250005071623 none CC(CNC(=O)CN(C)C)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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, 7]
0  hydrogens need rotated
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 27, 36, 36, 36, 94, 100, 100, 13, 8, 13, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 27, 27, 36, 94, 94, 100, 100, 100, 100, 100, 100, 15, 15, 13, 13, 13, 1] 100
rigid atoms, others: [41, 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])
total number of confs: 406
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071623 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071623
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071623/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071623/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071623
Building REAL250005071624
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071624'
/scratch/stefan/7916153/working/building/REAL250005071624 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071624

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071624/0 /scratch/stefan/7916153/working/building/REAL250005071624 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 762)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/762
`/scratch/stefan/7916153/working/3D/762' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(O)C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071624.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071624.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071624/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071624 none C=CC(O)C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 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]
1  hydrogens 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, 114, 201, 114, 114, 71, 40, 29, 40, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 114, 71, 71, 40, 40, 40, 40, 29, 29, 16, 16, 16, 1] 603
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: 1486
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071624 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071624
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071624/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071624
Building REAL250005071625
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071625'
/scratch/stefan/7916153/working/building/REAL250005071625 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071625

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071625/0 /scratch/stefan/7916153/working/building/REAL250005071625 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 763)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/763
`/scratch/stefan/7916153/working/3D/763' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1COC1)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071625.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071625.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071625/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071625 none CC(CNC(=O)C1COC1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
133  conformations in input
total number of sets (complete confs): 133
using faster count positions algorithm for large data
unique positions, atoms: [33, 28, 33, 62, 85, 85, 85, 133, 133, 133, 12, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 62, 62, 85, 133, 133, 133, 133, 133, 28, 28, 12, 12, 12, 1] 133
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: 510
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071625 none CC(CNC(=O)C1COC1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
133  conformations in input
total number of sets (complete confs): 133
using faster count positions algorithm for large data
unique positions, atoms: [53, 37, 9, 9, 1, 9, 1, 1, 1, 1, 55, 88, 94, 94, 127, 127, 133, 133, 133, 133, 133, 55, 55, 55, 55, 37, 37, 9, 1, 1, 1, 1, 1, 88, 88, 94, 94, 94, 133] 133
rigid atoms, others: [32, 4, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38])
total number of confs: 541
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071625 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071625
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071625/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071625
Building REAL250005071626
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071626'
/scratch/stefan/7916153/working/building/REAL250005071626 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071626

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071626/0 /scratch/stefan/7916153/working/building/REAL250005071626 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 764)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/764
`/scratch/stefan/7916153/working/3D/764' -> `0.mol2'
Preparing input files

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

`REAL250005071626.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071626.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071626/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071626 none CO[C@H](C)C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 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]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 27, 52, 52, 27, 27, 24, 17, 16, 17, 13, 7, 13, 1, 7, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 27, 24, 24, 17, 17, 17, 17, 16, 16, 13, 13, 13, 1] 52
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: 224
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071626 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071626
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071626/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071626
Building REAL250005071627
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071627'
/scratch/stefan/7916153/working/building/REAL250005071627 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071627

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071627/0 /scratch/stefan/7916153/working/building/REAL250005071627 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 765)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/765
`/scratch/stefan/7916153/working/3D/765' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=CC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071627.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071627.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071627/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071627 none CCC=CC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 142, 142, 96, 96, 96, 83, 48, 33, 48, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 142, 142, 96, 83, 83, 48, 48, 48, 48, 33, 33, 14, 14, 14, 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: 971
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071627 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071627
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071627/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071627
Building REAL250005071628
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071628'
/scratch/stefan/7916153/working/building/REAL250005071628 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL250005071628 as failed and skipping
/scratch/stefan/7916153/working /scratch/stefan/7916153
`/scratch/stefan/7916153/working/building/REAL250005071628' -> `/scratch/stefan/7916153/failed/REAL250005071628'
Building REAL250005071629
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071629'
/scratch/stefan/7916153/working/building/REAL250005071629 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071629

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071629/0 /scratch/stefan/7916153/working/building/REAL250005071629 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 766)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/766
`/scratch/stefan/7916153/working/3D/766' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)CO)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071629.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071629.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071629/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071629 none CC(CNC(=O)CO)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
384  conformations in input
total number of sets (complete confs): 384
using faster count positions algorithm for large data
unique positions, atoms: [63, 46, 63, 109, 128, 128, 128, 128, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 109, 109, 128, 128, 128, 384, 46, 46, 15, 15, 15, 1] 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])
total number of confs: 948
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071629 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071629
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071629/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071629
Building REAL250005071630
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071630'
/scratch/stefan/7916153/working/building/REAL250005071630 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071630

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071630/0 /scratch/stefan/7916153/working/building/REAL250005071630 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 767)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/767
`/scratch/stefan/7916153/working/3D/767' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071630.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071630.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071630/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071630 none CC(O)C(=O)NCC(C)CN(C)C(=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', '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']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 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, 7, 6, 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
483  conformations in input
total number of sets (complete confs): 483
using faster count positions algorithm for large data
unique positions, atoms: [161, 158, 161, 158, 158, 122, 57, 41, 57, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 483, 158, 122, 122, 57, 57, 57, 57, 41, 41, 15, 15, 15, 1] 483
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: 1179
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071630 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071630
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071630/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071630
Building REAL250005071631
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071631'
/scratch/stefan/7916153/working/building/REAL250005071631 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071631

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071631/0 /scratch/stefan/7916153/working/building/REAL250005071631 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 768)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/768
`/scratch/stefan/7916153/working/3D/768' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1CC1F)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071631.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071631.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071631/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071631 none CC(CNC(=O)C1CC1F)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [47, 34, 47, 101, 142, 142, 142, 192, 192, 192, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 101, 101, 142, 192, 192, 192, 192, 34, 34, 13, 13, 13, 1] 192
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: 755
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071631 none CC(CNC(=O)C1CC1F)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [75, 37, 10, 10, 1, 10, 1, 1, 1, 1, 73, 127, 149, 149, 185, 185, 192, 192, 192, 192, 192, 77, 77, 77, 77, 37, 37, 10, 1, 1, 1, 1, 126, 127, 149, 149, 149, 192] 192
rigid atoms, others: [4, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37])
total number of confs: 812
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071631 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071631
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071631/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071631
Building REAL250005071632
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071632'
/scratch/stefan/7916153/working/building/REAL250005071632 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071632

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071632/0 /scratch/stefan/7916153/working/building/REAL250005071632 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 769)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/769
`/scratch/stefan/7916153/working/3D/769' -> `0.mol2'
Preparing input files

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

`REAL250005071632.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071632.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071632/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071632 none CC(CNC(=O)CCF)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', '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, 5, 5, 8, 1, 11, 5, 5, 15, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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: [45, 35, 45, 84, 124, 124, 124, 201, 201, 15, 7, 15, 1, 7, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 84, 84, 124, 201, 201, 201, 201, 35, 35, 15, 15, 15, 1] 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])
total number of confs: 865
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071632 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071632
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071632/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071632
Building REAL250005071633
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071633'
/scratch/stefan/7916153/working/building/REAL250005071633 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071633

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071633/0 /scratch/stefan/7916153/working/building/REAL250005071633 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 770)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/770
`/scratch/stefan/7916153/working/3D/770' -> `0.mol2'
Preparing input files

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

`REAL250005071633.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071633.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071633/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071633 none CC(CNC(=O)C=CCF)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', '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, 5, 5, 8, 1, 11, 1, 1, 5, 15, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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: [35, 27, 35, 78, 117, 117, 117, 194, 194, 201, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 78, 78, 117, 194, 194, 201, 201, 27, 27, 14, 14, 14, 1] 201
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: 767
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071633 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071633
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071633/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071633
Building REAL250005071634
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071634'
/scratch/stefan/7916153/working/building/REAL250005071634 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071634

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071634/0 /scratch/stefan/7916153/working/building/REAL250005071634 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 771)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/771
`/scratch/stefan/7916153/working/3D/771' -> `0.mol2'
Preparing input files

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

`REAL250005071634.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071634.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071634/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071634 none C#CCCC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 5, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
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, 120, 120, 120, 91, 49, 35, 49, 15, 7, 15, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 194, 194, 120, 91, 91, 49, 49, 49, 49, 35, 35, 15, 15, 15, 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: 889
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071634 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071634
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071634/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071634
Building REAL250005071635
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071635'
/scratch/stefan/7916153/working/building/REAL250005071635 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071635

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071635/0 /scratch/stefan/7916153/working/building/REAL250005071635 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 772)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/772
`/scratch/stefan/7916153/working/3D/772' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1CCO1)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071635.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071635.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071635/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071635 none CC(CNC(=O)C1CCO1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 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: [66, 48, 66, 132, 179, 179, 179, 182, 182, 182, 16, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 132, 132, 179, 182, 182, 182, 182, 182, 48, 48, 16, 16, 16, 1] 182
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: 761
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071635 none CC(CNC(=O)C1CCO1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 6, 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: [62, 22, 5, 5, 1, 5, 1, 1, 1, 1, 63, 113, 141, 141, 178, 178, 182, 182, 182, 182, 182, 67, 67, 67, 67, 22, 22, 5, 1, 1, 1, 1, 1, 112, 113, 141, 141, 141, 182] 182
rigid atoms, others: [32, 4, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38])
total number of confs: 766
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071635 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071635
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071635/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071635
Building REAL250005071636
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071636'
/scratch/stefan/7916153/working/building/REAL250005071636 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071636

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071636/0 /scratch/stefan/7916153/working/building/REAL250005071636 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 773)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/773
`/scratch/stefan/7916153/working/3D/773' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C(C)(C)O)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071636.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071636.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071636/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071636 none CC(CNC(=O)C(C)(C)O)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 5, 5, 12, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [63, 43, 63, 125, 167, 167, 167, 201, 201, 201, 17, 8, 17, 1, 8, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 125, 125, 167, 201, 201, 201, 201, 201, 201, 603, 43, 43, 17, 17, 17, 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: 1505
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071636 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071636
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071636/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071636
Building REAL250005071637
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071637'
/scratch/stefan/7916153/working/building/REAL250005071637 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071637

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071637/0 /scratch/stefan/7916153/working/building/REAL250005071637 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 774)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/774
`/scratch/stefan/7916153/working/3D/774' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071637.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071637.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071637/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071637 none CC1=CC1C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 1, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 100, 100, 100, 65, 36, 30, 36, 11, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 100, 65, 65, 36, 36, 36, 36, 30, 30, 11, 11, 11, 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: 721
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071637 none CC1=CC1C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 1, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
201  conformations in 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, 45, 77, 81, 122, 140, 140, 193, 193, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 13, 45, 45, 81, 81, 81, 81, 122, 122, 140, 140, 140, 201] 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, 37, 38])
total number of confs: 828
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071637 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071637
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071637/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071637
Building REAL250005071638
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071638'
/scratch/stefan/7916153/working/building/REAL250005071638 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071638

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071638/0 /scratch/stefan/7916153/working/building/REAL250005071638 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 775)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/775
`/scratch/stefan/7916153/working/3D/775' -> `0.mol2'
Preparing input files

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

`REAL250005071638.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071638.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071638/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071638 none CC(CNC(=O)[C@@H](C)O)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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, 7, 7]
1  hydrogens need rotated
540  conformations in input
total number of sets (complete confs): 540
using faster count positions algorithm for large data
unique positions, atoms: [66, 44, 66, 130, 175, 175, 175, 180, 180, 180, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 130, 130, 175, 180, 180, 180, 540, 44, 44, 15, 15, 15, 1] 540
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: 1321
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071638 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071638
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071638/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071638
Building REAL250005071639
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071639'
/scratch/stefan/7916153/working/building/REAL250005071639 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071639

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071639/0 /scratch/stefan/7916153/working/building/REAL250005071639 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 776)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/776
`/scratch/stefan/7916153/working/3D/776' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C=CCO)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071639.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071639.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071639/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071639 none CC(CNC(=O)C=CCO)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.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, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 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, 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, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [28, 23, 28, 59, 93, 93, 93, 183, 183, 201, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 59, 59, 93, 183, 183, 201, 201, 603, 23, 23, 14, 14, 14, 1] 603
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: 1368
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071639 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071639
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071639/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071639
Building REAL250005071640
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071640'
/scratch/stefan/7916153/working/building/REAL250005071640 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071640

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071640/0 /scratch/stefan/7916153/working/building/REAL250005071640 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 777)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/777
`/scratch/stefan/7916153/working/3D/777' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CCC1)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071640.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071640.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071640/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071640 none CC(CNC(=O)C1=CCC1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [37, 28, 37, 66, 80, 80, 80, 80, 80, 80, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 66, 66, 80, 80, 80, 80, 80, 80, 28, 28, 13, 13, 13, 1] 80
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: 351
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071640 none CC(CNC(=O)C1=CCC1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [29, 15, 3, 3, 1, 3, 1, 1, 1, 1, 29, 50, 65, 65, 78, 78, 80, 80, 80, 80, 80, 31, 31, 31, 31, 15, 15, 3, 1, 1, 1, 1, 1, 49, 50, 65, 65, 65, 80] 80
rigid atoms, others: [32, 4, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38])
total number of confs: 328
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071640 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071640
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071640/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071640
Building REAL250005071641
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071641'
/scratch/stefan/7916153/working/building/REAL250005071641 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071641

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071641/0 /scratch/stefan/7916153/working/building/REAL250005071641 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 778)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/778
`/scratch/stefan/7916153/working/3D/778' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=CC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071641.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071641.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071641/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071641 none CON=CC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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]
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, 12, 12, 12, 11, 10, 8, 10, 8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 12, 11, 11, 10, 10, 10, 10, 8, 8, 8, 8, 8, 1] 19
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: 67
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071641 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071641
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071641/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071641
Building REAL250005071642
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071642'
/scratch/stefan/7916153/working/building/REAL250005071642 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071642

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071642/0 /scratch/stefan/7916153/working/building/REAL250005071642 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 779)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/779
`/scratch/stefan/7916153/working/3D/779' -> `0.mol2'
Preparing input files

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

`REAL250005071642.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071642.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071642/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071642 none CC(CNC(=O)C1(F)CC1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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: [61, 44, 61, 120, 174, 174, 174, 201, 201, 201, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 120, 120, 174, 201, 201, 201, 201, 44, 44, 15, 15, 15, 1] 201
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: 822
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071642 none CC(CNC(=O)C1(F)CC1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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: [76, 40, 8, 8, 1, 8, 1, 1, 1, 1, 76, 122, 149, 149, 196, 196, 201, 201, 201, 201, 201, 78, 78, 78, 78, 40, 40, 8, 1, 1, 1, 1, 122, 121, 149, 149, 149, 201] 201
rigid atoms, others: [4, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37])
total number of confs: 837
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071642 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071642
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071642/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071642
Building REAL250005071643
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071643'
/scratch/stefan/7916153/working/building/REAL250005071643 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071643

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071643/0 /scratch/stefan/7916153/working/building/REAL250005071643 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 780)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/780
`/scratch/stefan/7916153/working/3D/780' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(F)C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071643.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071643.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071643/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071643 none CC=C(F)C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [118, 118, 118, 118, 118, 118, 89, 50, 39, 50, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 118, 89, 89, 50, 50, 50, 50, 39, 39, 15, 15, 15, 1] 118
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: 500
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071643 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071643
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071643/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071643
Building REAL250005071644
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071644'
/scratch/stefan/7916153/working/building/REAL250005071644 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071644

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071644/0 /scratch/stefan/7916153/working/building/REAL250005071644 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 781)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/781
`/scratch/stefan/7916153/working/3D/781' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C(C)CO)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071644.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071644.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071644/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071644 none CC(CNC(=O)C(C)CO)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 5, 5, 12, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 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, 7, 7, 7, 7, 7]
1  hydrogens 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, 32, 36, 74, 111, 111, 111, 200, 200, 201, 19, 9, 19, 1, 9, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 74, 74, 111, 200, 200, 200, 200, 201, 201, 603, 32, 32, 19, 19, 19, 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: 1445
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071644 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071644
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071644/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071644
Building REAL250005071645
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071645'
/scratch/stefan/7916153/working/building/REAL250005071645 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071645

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071645/0 /scratch/stefan/7916153/working/building/REAL250005071645 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 782)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/782
`/scratch/stefan/7916153/working/3D/782' -> `0.mol2'
Preparing input files

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

`REAL250005071645.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071645.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071645/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071645 none CC(CNC(=O)[C@H](C)O)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 7, 5, 12, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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, 7, 7]
1  hydrogens need rotated
492  conformations in input
total number of sets (complete confs): 492
using faster count positions algorithm for large data
unique positions, atoms: [57, 41, 57, 124, 161, 161, 161, 164, 164, 164, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 124, 124, 161, 164, 164, 164, 492, 41, 41, 15, 15, 15, 1] 492
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: 1196
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071645 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071645
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071645/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071645
Building REAL250005071646
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071646'
/scratch/stefan/7916153/working/building/REAL250005071646 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071646

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071646/0 /scratch/stefan/7916153/working/building/REAL250005071646 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 783)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/783
`/scratch/stefan/7916153/working/3D/783' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071646.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071646.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071646/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071646 none C=C1CC1C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 5, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
201  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, 98, 44, 34, 44, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 140, 98, 98, 44, 44, 44, 44, 34, 34, 13, 13, 13, 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: 782
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071646 none C=C1CC1C(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 5, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 11, 39, 76, 77, 130, 151, 151, 192, 192, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 11, 39, 39, 78, 78, 78, 78, 129, 130, 151, 151, 151, 201] 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, 37, 38])
total number of confs: 848
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071646 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071646
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071646/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071646
Building REAL250005071647
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071647'
/scratch/stefan/7916153/working/building/REAL250005071647 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071647

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071647/0 /scratch/stefan/7916153/working/building/REAL250005071647 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 784)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/784
`/scratch/stefan/7916153/working/3D/784' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071647.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071647.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071647/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071647 none C=C(C)CC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1 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.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, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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
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, 16, 16, 16, 14, 12, 11, 12, 10, 7, 10, 1, 7, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 16, 14, 14, 12, 12, 12, 12, 11, 11, 10, 10, 10, 1] 39
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: 160
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071647 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071647
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071647/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071647
Building REAL250005071648
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071648'
/scratch/stefan/7916153/working/building/REAL250005071648 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071648

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071648/0 /scratch/stefan/7916153/working/building/REAL250005071648 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 785)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/785
`/scratch/stefan/7916153/working/3D/785' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)NCC(C)CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071648.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071648.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071648/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071648 none CC=CC(=O)NCC(C)CN(C)C(=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', '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']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 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]
dock color type numbers: [7, 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]
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, 71, 71, 71, 58, 37, 28, 37, 12, 6, 12, 1, 6, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 71, 58, 58, 37, 37, 37, 37, 28, 28, 12, 12, 12, 1] 103
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: 443
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071648 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071648
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071648/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071648
Building REAL250005071649
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071649'
/scratch/stefan/7916153/working/building/REAL250005071649 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071649

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071649/0 /scratch/stefan/7916153/working/building/REAL250005071649 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 786)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/786
`/scratch/stefan/7916153/working/3D/786' -> `0.mol2'
Preparing input files

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

`REAL250005071649.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071649.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071649/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071649 none CC(CNC(=O)[C@@H]1C[C@H]1C)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
189  conformations in input
total number of sets (complete confs): 189
using faster count positions algorithm for large data
unique positions, atoms: [44, 32, 44, 84, 112, 112, 112, 189, 189, 189, 189, 189, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 84, 84, 112, 189, 189, 189, 189, 189, 32, 32, 13, 13, 13, 1] 189
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: 742
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071649 none CC(CNC(=O)[C@@H]1C[C@H]1C)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
189  conformations in input
total number of sets (complete confs): 189
using faster count positions algorithm for large data
unique positions, atoms: [68, 35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 71, 116, 138, 138, 177, 177, 189, 189, 189, 189, 189, 72, 72, 72, 72, 35, 35, 11, 1, 1, 2, 2, 2, 115, 116, 138, 138, 138, 189] 189
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 777
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071649 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071649
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071649/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071649
Building REAL250005071650
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071650'
/scratch/stefan/7916153/working/building/REAL250005071650 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071650

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071650/0 /scratch/stefan/7916153/working/building/REAL250005071650 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 787)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/787
`/scratch/stefan/7916153/working/3D/787' -> `0.mol2'
Preparing input files

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

`REAL250005071650.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071650.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071650/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071650 none CC(CNC(=O)C1(O)CC1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 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, 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]
1  hydrogens need rotated
597  conformations in input
total number of sets (complete confs): 597
using faster count positions algorithm for large data
unique positions, atoms: [65, 46, 65, 123, 179, 179, 179, 199, 199, 199, 16, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 123, 123, 179, 597, 199, 199, 199, 199, 46, 46, 16, 16, 16, 1] 597
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: 1400
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071650 none CC(CNC(=O)C1(O)CC1)CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 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, 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]
1  hydrogens need rotated
597  conformations in input
total number of sets (complete confs): 597
using faster count positions algorithm for large data
unique positions, atoms: [66, 35, 8, 8, 1, 8, 1, 1, 1, 1, 68, 120, 150, 150, 195, 195, 199, 199, 199, 199, 199, 70, 70, 70, 70, 35, 35, 8, 6, 1, 1, 1, 1, 120, 119, 150, 150, 150, 199] 597
rigid atoms, others: [32, 4, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 3, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38])
total number of confs: 845
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071650 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071650
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071650/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071650
Building REAL250005071651
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071651'
/scratch/stefan/7916153/working/building/REAL250005071651 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071651

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071651/0 /scratch/stefan/7916153/working/building/REAL250005071651 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 788)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/788
`/scratch/stefan/7916153/working/3D/788' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)CC1CC1)

`REAL250005071651.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071651.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071651/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071651 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)CC1CC1 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 7, 7, 7]
0  hydrogens 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, 69, 85, 158, 201, 201, 201, 201, 201, 201, 201, 201, 34, 17, 34, 3, 17, 1, 1, 1, 1, 85, 85, 85, 85, 158, 158, 201, 201, 69, 69, 34, 34, 34, 3, 3, 1, 1, 1, 1, 1] 201
rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 846
number of broken/clashed sets: 49
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071651 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)CC1CC1 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 39, 66, 97, 97, 134, 134, 154, 201, 201, 41, 41, 41, 41, 15, 15, 4, 1, 66, 66, 97, 97, 97, 154, 154, 201, 201, 201, 201, 201] 201
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 845
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071651 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071651
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071651/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071651
Building REAL250005071652
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071652'
/scratch/stefan/7916153/working/building/REAL250005071652 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071652

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071652/0 /scratch/stefan/7916153/working/building/REAL250005071652 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 789)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/789
`/scratch/stefan/7916153/working/3D/789' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005071652.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071652.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071652/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071652 none COCC(=O)N(C)CC(C)CNC(=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', 'C.3', '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, 12, 5, 1, 11, 8, 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, 6, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 187, 114, 96, 114, 71, 96, 40, 15, 36, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 187, 187, 96, 96, 96, 71, 71, 42, 42, 42, 42, 15, 15, 4, 1] 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])
total number of confs: 921
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071652 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071652
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071652/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071652
Building REAL250005071653
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071653'
/scratch/stefan/7916153/working/building/REAL250005071653 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071653

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071653/0 /scratch/stefan/7916153/working/building/REAL250005071653 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 790)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/790
`/scratch/stefan/7916153/working/3D/790' -> `0.mol2'
Preparing input files

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

`REAL250005071653.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071653.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071653/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071653 none CCCC(=O)N(C)CC(C)CNC(=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', 'C.3', '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, 5, 5, 1, 11, 8, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 137, 110, 137, 77, 110, 38, 13, 36, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 110, 110, 110, 77, 76, 40, 40, 40, 40, 13, 13, 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: 871
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071653 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071653
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071653/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071653
Building REAL250005071654
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071654'
/scratch/stefan/7916153/working/building/REAL250005071654 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071654

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071654/0 /scratch/stefan/7916153/working/building/REAL250005071654 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 791)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/791
`/scratch/stefan/7916153/working/3D/791' -> `0.mol2'
Preparing input files

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

`REAL250005071654.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071654.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071654/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071654 none CC(C)CC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 5, 1, 11, 8, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 127, 159, 96, 127, 50, 18, 48, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127, 127, 96, 94, 54, 54, 54, 54, 18, 18, 4, 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: 913
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071654 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071654
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071654/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071654
Building REAL250005071655
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071655'
/scratch/stefan/7916153/working/building/REAL250005071655 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071655

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071655/0 /scratch/stefan/7916153/working/building/REAL250005071655 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 792)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/792
`/scratch/stefan/7916153/working/3D/792' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1CC1C)

`REAL250005071655.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071655.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071655/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071655 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1CC1C 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [44, 34, 44, 85, 107, 107, 107, 107, 107, 107, 107, 107, 14, 8, 14, 1, 8, 1, 1, 1, 1, 44, 44, 44, 44, 85, 85, 107, 107, 34, 34, 14, 14, 14, 1, 1, 1, 1, 2, 2, 2] 107
rigid atoms, others: [34, 35, 36, 37, 15, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40])
total number of confs: 468
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071655 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1CC1C 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [34, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 33, 47, 64, 64, 78, 78, 107, 107, 107, 35, 35, 35, 35, 14, 14, 4, 1, 46, 47, 64, 64, 64, 107, 107, 107, 107, 107, 107, 107] 107
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 434
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071655 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071655
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071655/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071655
Building REAL250005071656
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071656'
/scratch/stefan/7916153/working/building/REAL250005071656 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071656

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071656/0 /scratch/stefan/7916153/working/building/REAL250005071656 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 793)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/793
`/scratch/stefan/7916153/working/3D/793' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005071656.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071656.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071656/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071656 none CCOCC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 12, 5, 1, 11, 8, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 161, 84, 81, 84, 66, 81, 37, 16, 39, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 161, 161, 81, 81, 81, 66, 66, 39, 39, 39, 39, 16, 16, 4, 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: 812
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071656 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071656
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071656/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071656
Building REAL250005071657
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071657'
/scratch/stefan/7916153/working/building/REAL250005071657 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071657

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071657/0 /scratch/stefan/7916153/working/building/REAL250005071657 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 794)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/794
`/scratch/stefan/7916153/working/3D/794' -> `0.mol2'
Preparing input files

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

`REAL250005071657.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071657.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071657/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071657 none CC(C)=CC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 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', '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, 5, 1, 1, 11, 8, 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, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 145, 117, 145, 81, 117, 41, 16, 39, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 117, 117, 117, 81, 80, 44, 44, 44, 44, 16, 16, 4, 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: 847
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071657 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071657
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071657/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071657
Building REAL250005071658
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071658'
/scratch/stefan/7916153/working/building/REAL250005071658 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071658

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071658/0 /scratch/stefan/7916153/working/building/REAL250005071658 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 795)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/795
`/scratch/stefan/7916153/working/3D/795' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005071658.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071658.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071658/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071658 none CCCCC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 5, 1, 11, 8, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 196, 115, 98, 115, 75, 98, 37, 12, 36, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 199, 199, 196, 196, 98, 98, 98, 75, 74, 40, 40, 40, 40, 12, 12, 3, 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: 887
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071658 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071658
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071658/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071658
Building REAL250005071659
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071659'
/scratch/stefan/7916153/working/building/REAL250005071659 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071659

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071659/0 /scratch/stefan/7916153/working/building/REAL250005071659 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 796)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/796
`/scratch/stefan/7916153/working/3D/796' -> `0.mol2'
Preparing input files

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

`REAL250005071659.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071659.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071659/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071659 none CC(C)C(=O)N(C)CC(C)CNC(=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', 'C.3', '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, 5, 5, 1, 11, 8, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 83, 97, 56, 83, 33, 16, 33, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 97, 97, 97, 83, 83, 83, 56, 56, 35, 35, 35, 35, 16, 16, 4, 1] 97
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: 404
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071659 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071659
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071659/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071659
Building REAL250005071660
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071660'
/scratch/stefan/7916153/working/building/REAL250005071660 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071660

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071660/0 /scratch/stefan/7916153/working/building/REAL250005071660 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 797)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/797
`/scratch/stefan/7916153/working/3D/797' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005071660.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071660.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071660/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071660 none CCC(C)C(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 5, 1, 11, 8, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 194, 161, 194, 138, 161, 107, 138, 55, 21, 54, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 194, 194, 194, 194, 138, 138, 138, 107, 106, 59, 59, 59, 59, 21, 21, 4, 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: 916
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071660 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071660
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071660/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071660
Building REAL250005071661
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071661'
/scratch/stefan/7916153/working/building/REAL250005071661 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071661

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071661/0 /scratch/stefan/7916153/working/building/REAL250005071661 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 798)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/798
`/scratch/stefan/7916153/working/3D/798' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005071661.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071661.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071661/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071661 none COC(C)C(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 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', '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, 12, 5, 5, 1, 11, 8, 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, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 168, 195, 139, 168, 103, 139, 59, 21, 60, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 195, 195, 195, 139, 139, 139, 103, 102, 66, 66, 66, 66, 21, 21, 4, 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: 897
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071661 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071661
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071661/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071661
Building REAL250005071662
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071662'
/scratch/stefan/7916153/working/building/REAL250005071662 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071662

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071662/0 /scratch/stefan/7916153/working/building/REAL250005071662 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 799)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/799
`/scratch/stefan/7916153/working/3D/799' -> `0.mol2'
Preparing input files

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

`REAL250005071662.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071662.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071662/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071662 none C=CCCC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 119, 96, 119, 70, 96, 34, 13, 33, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 96, 96, 96, 70, 70, 38, 38, 38, 38, 13, 13, 4, 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: 902
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071662 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071662
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071662/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071662
Building REAL250005071663
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071663'
/scratch/stefan/7916153/working/building/REAL250005071663 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071663

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071663/0 /scratch/stefan/7916153/working/building/REAL250005071663 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 800)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/800
`/scratch/stefan/7916153/working/3D/800' -> `0.mol2'
Preparing input files

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

`REAL250005071663.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071663.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071663/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071663 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C(C)C#N 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [35, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 34, 54, 62, 62, 72, 72, 75, 75, 75, 36, 36, 36, 36, 13, 13, 4, 1, 54, 53, 62, 62, 62, 75, 75, 75, 75] 75
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 322
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071663 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071663
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071663/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071663
Building REAL250005071664
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071664'
/scratch/stefan/7916153/working/building/REAL250005071664 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071664

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071664/0 /scratch/stefan/7916153/working/building/REAL250005071664 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 801)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/801
`/scratch/stefan/7916153/working/3D/801' -> `0.mol2'
Preparing input files

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

`REAL250005071664.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071664.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071664/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071664 none CC=C(C)C(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 107, 132, 78, 107, 34, 10, 34, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 107, 107, 107, 78, 77, 37, 37, 37, 37, 10, 10, 3, 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: 834
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071664 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071664
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071664/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071664
Building REAL250005071665
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071665'
/scratch/stefan/7916153/working/building/REAL250005071665 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071665

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071665/0 /scratch/stefan/7916153/working/building/REAL250005071665 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 802)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/802
`/scratch/stefan/7916153/working/3D/802' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005071665.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071665.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071665/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071665 none CCC(=O)N(C)CC(C)CNC(=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', '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, 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, 6, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [136, 129, 108, 129, 76, 108, 41, 17, 42, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 136, 108, 108, 108, 76, 74, 44, 44, 44, 44, 17, 17, 4, 1] 136
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])
total number of confs: 570
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071665 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071665
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071665/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071665
Building REAL250005071666
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071666'
/scratch/stefan/7916153/working/building/REAL250005071666 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071666

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071666/0 /scratch/stefan/7916153/working/building/REAL250005071666 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 803)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/803
`/scratch/stefan/7916153/working/3D/803' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005071666.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071666.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071666/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071666 none COCCC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 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', '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, 12, 5, 5, 1, 11, 8, 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, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 194, 137, 109, 137, 75, 109, 35, 13, 36, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 198, 198, 194, 194, 109, 109, 109, 75, 75, 39, 39, 39, 39, 13, 13, 3, 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: 898
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071666 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071666
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071666/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071666
Building REAL250005071667
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071667'
/scratch/stefan/7916153/working/building/REAL250005071667 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071667

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071667/0 /scratch/stefan/7916153/working/building/REAL250005071667 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 804)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/804
`/scratch/stefan/7916153/working/3D/804' -> `0.mol2'
Preparing input files

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

`REAL250005071667.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071667.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071667/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071667 none CC(=O)N(C)CC(C)CNC(=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', '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, 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, 6, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [144, 134, 144, 112, 134, 70, 31, 70, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 144, 144, 144, 134, 134, 134, 112, 111, 73, 73, 73, 73, 31, 31, 10, 1] 144
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])
total number of confs: 599
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071667 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071667
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071667/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071667
Building REAL250005071668
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071668'
/scratch/stefan/7916153/working/building/REAL250005071668 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071668

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071668/0 /scratch/stefan/7916153/working/building/REAL250005071668 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 805)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/805
`/scratch/stefan/7916153/working/3D/805' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1CC1)

`REAL250005071668.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071668.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071668/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071668 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1CC1 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 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, 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
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [38, 30, 38, 80, 98, 98, 98, 98, 98, 98, 98, 98, 13, 8, 13, 1, 8, 1, 1, 1, 38, 38, 38, 38, 80, 80, 98, 98, 30, 30, 13, 13, 13, 1, 1, 1, 1, 1] 98
rigid atoms, others: [33, 34, 35, 36, 37, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 420
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071668 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1CC1 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 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, 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
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [31, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 30, 42, 56, 56, 66, 66, 98, 98, 32, 32, 32, 32, 14, 14, 4, 1, 42, 41, 56, 56, 56, 98, 98, 98, 98, 98] 98
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, 37])
total number of confs: 400
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071668 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071668
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071668/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071668
Building REAL250005071669
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071669'
/scratch/stefan/7916153/working/building/REAL250005071669 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071669

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071669/0 /scratch/stefan/7916153/working/building/REAL250005071669 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 806)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/806
`/scratch/stefan/7916153/working/3D/806' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1CCC1)

`REAL250005071669.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071669.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071669/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071669 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1CCC1 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [58, 46, 58, 110, 143, 143, 143, 143, 143, 143, 143, 143, 18, 8, 18, 1, 8, 1, 1, 1, 1, 58, 58, 58, 58, 110, 110, 143, 143, 46, 46, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1] 143
rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 15, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 591
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071669 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1CCC1 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [33, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 33, 62, 83, 83, 104, 104, 143, 143, 143, 35, 35, 35, 35, 17, 17, 4, 1, 62, 61, 83, 83, 83, 143, 143, 143, 143, 143, 143, 143] 143
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 593
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071669 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071669
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071669/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071669
Building REAL250005071670
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071670'
/scratch/stefan/7916153/working/building/REAL250005071670 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071670

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071670/0 /scratch/stefan/7916153/working/building/REAL250005071670 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 807)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/807
`/scratch/stefan/7916153/working/3D/807' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C(N)=O)

`REAL250005071670.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071670.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071670/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071670 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C(N)=O 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.3', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [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, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [13, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 18, 22, 22, 23, 23, 27, 27, 13, 13, 13, 13, 7, 7, 2, 1, 18, 18, 22, 22, 22, 27, 27] 27
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])
total number of confs: 114
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071670 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071670
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071670/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071670
Building REAL250005071671
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071671'
/scratch/stefan/7916153/working/building/REAL250005071671 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071671

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071671/0 /scratch/stefan/7916153/working/building/REAL250005071671 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 808)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/808
`/scratch/stefan/7916153/working/3D/808' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C(C)(C)C)

`REAL250005071671.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071671.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071671/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071671 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C(C)(C)C 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [43, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 42, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 27, 27, 7, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 44
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 193
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071671 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071671
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071671/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071671
Building REAL250005071672
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071672'
/scratch/stefan/7916153/working/building/REAL250005071672 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071672

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071672/0 /scratch/stefan/7916153/working/building/REAL250005071672 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 809)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/809
`/scratch/stefan/7916153/working/3D/809' -> `0.mol2'
Preparing input files

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

`REAL250005071672.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071672.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071672/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071672 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1(C)CC1 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 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: [11, 9, 11, 20, 27, 27, 27, 27, 27, 27, 27, 27, 6, 3, 6, 1, 3, 1, 1, 1, 1, 11, 11, 11, 11, 20, 20, 27, 27, 9, 9, 6, 6, 6, 2, 2, 2, 1, 1, 1, 1] 27
rigid atoms, others: [37, 38, 39, 40, 15, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 112
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071672 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1(C)CC1 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [19, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 17, 22, 26, 26, 27, 27, 27, 27, 27, 19, 19, 19, 19, 10, 10, 3, 1, 22, 21, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27] 27
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 114
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071672 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071672
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071672/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071672
Building REAL250005071673
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071673'
/scratch/stefan/7916153/working/building/REAL250005071673 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071673

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071673/0 /scratch/stefan/7916153/working/building/REAL250005071673 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 810)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/810
`/scratch/stefan/7916153/working/3D/810' -> `0.mol2'
Preparing input files

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

`REAL250005071673.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071673.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071673/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071673 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)[C@@H]1C[C@H]1C 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.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 7, 5, 5, 7, 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, 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, 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: [40, 30, 40, 75, 95, 95, 95, 95, 95, 95, 95, 95, 12, 7, 12, 1, 7, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 75, 75, 95, 95, 30, 30, 12, 12, 12, 1, 1, 2, 2, 2] 95
rigid atoms, others: [36, 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, 38, 39, 40])
total number of confs: 415
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071673 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)[C@@H]1C[C@H]1C 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.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 7, 5, 5, 7, 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, 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, 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: [28, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 38, 54, 54, 65, 65, 95, 95, 95, 95, 95, 28, 28, 28, 28, 11, 11, 2, 1, 38, 38, 54, 54, 54, 95, 95, 95, 95, 95] 95
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 387
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071673 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071673
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071673/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071673
Building REAL250005071674
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071674'
/scratch/stefan/7916153/working/building/REAL250005071674 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071674

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071674/0 /scratch/stefan/7916153/working/building/REAL250005071674 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 811)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/811
`/scratch/stefan/7916153/working/3D/811' -> `0.mol2'
Preparing input files

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

`REAL250005071674.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071674.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071674/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071674 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)[C@H]1C[C@@H]1C 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.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 7, 5, 5, 7, 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, 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, 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: [42, 33, 42, 84, 106, 106, 106, 106, 106, 106, 106, 106, 13, 8, 13, 1, 8, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 84, 84, 106, 106, 33, 33, 13, 13, 13, 1, 1, 2, 2, 2] 106
rigid atoms, others: [36, 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, 38, 39, 40])
total number of confs: 461
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071674 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)[C@H]1C[C@@H]1C 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.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 7, 5, 5, 7, 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, 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, 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: [32, 13, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 31, 46, 63, 63, 77, 77, 106, 106, 106, 106, 106, 33, 33, 33, 33, 13, 13, 3, 1, 46, 45, 63, 63, 63, 106, 106, 106, 106, 106] 106
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 435
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071674 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071674
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071674/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071674
Building REAL250005071675
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071675'
/scratch/stefan/7916153/working/building/REAL250005071675 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071675

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071675/0 /scratch/stefan/7916153/working/building/REAL250005071675 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 812)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/812
`/scratch/stefan/7916153/working/3D/812' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)CO)

`REAL250005071675.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071675.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071675/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071675 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)CO 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.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
333  conformations in input
total number of sets (complete confs): 333
using faster count positions algorithm for large data
unique positions, atoms: [39, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 39, 68, 88, 88, 99, 99, 111, 41, 41, 41, 41, 16, 16, 4, 1, 68, 68, 88, 88, 88, 111, 111, 333] 333
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 26] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 822
number of broken/clashed sets: 130
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071675 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071675
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071675/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071675
Building REAL250005071676
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071676'
/scratch/stefan/7916153/working/building/REAL250005071676 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071676

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071676/0 /scratch/stefan/7916153/working/building/REAL250005071676 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 813)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/813
`/scratch/stefan/7916153/working/3D/813' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1CCO1)

`REAL250005071676.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071676.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071676/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071676 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1CCO1 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [28, 23, 28, 48, 58, 58, 58, 58, 58, 58, 58, 58, 11, 5, 11, 1, 5, 1, 1, 1, 1, 28, 28, 28, 28, 48, 48, 58, 58, 23, 23, 11, 11, 11, 1, 1, 1, 1, 1] 58
rigid atoms, others: [34, 35, 36, 37, 38, 15, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 225
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071676 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1CCO1 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [24, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 39, 48, 48, 57, 57, 58, 58, 58, 25, 25, 25, 25, 9, 9, 2, 1, 39, 39, 48, 48, 48, 58, 58, 58, 58, 58] 58
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 259
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071676 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071676
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071676/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071676
Building REAL250005071677
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071677'
/scratch/stefan/7916153/working/building/REAL250005071677 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071677

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071677/0 /scratch/stefan/7916153/working/building/REAL250005071677 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 814)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/814
`/scratch/stefan/7916153/working/3D/814' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1COC1)

`REAL250005071677.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071677.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071677/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071677 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1COC1 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 12, 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, 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, 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: [62, 47, 62, 116, 144, 144, 144, 144, 144, 144, 144, 144, 18, 8, 18, 1, 8, 1, 1, 1, 1, 62, 62, 62, 62, 116, 116, 144, 144, 47, 47, 18, 18, 18, 1, 1, 1, 1, 1] 144
rigid atoms, others: [34, 35, 36, 37, 38, 15, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 600
number of broken/clashed sets: 35
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071677 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1COC1 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 12, 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, 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, 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: [36, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 64, 88, 88, 109, 109, 144, 144, 144, 38, 38, 38, 38, 16, 16, 4, 1, 63, 64, 88, 88, 88, 144, 144, 144, 144, 144] 144
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 599
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071677 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071677
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071677/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071677
Building REAL250005071678
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071678'
/scratch/stefan/7916153/working/building/REAL250005071678 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071678

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071678/0 /scratch/stefan/7916153/working/building/REAL250005071678 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 815)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/815
`/scratch/stefan/7916153/working/3D/815' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C=CCO)

`REAL250005071678.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071678.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071678/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071678 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C=CCO 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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 7, 7, 7]
1  hydrogens 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, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 34, 58, 93, 93, 135, 135, 197, 197, 201, 36, 36, 36, 36, 14, 14, 4, 1, 58, 57, 93, 93, 93, 197, 197, 201, 201, 603] 603
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 1373
number of broken/clashed sets: 55
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071678 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071678
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071678/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071678
Building REAL250005071679
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071679'
/scratch/stefan/7916153/working/building/REAL250005071679 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071679

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071679/0 /scratch/stefan/7916153/working/building/REAL250005071679 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 816)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/816
`/scratch/stefan/7916153/working/3D/816' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=CC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005071679.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071679.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071679/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071679 none CCC=CC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 1, 1, 1, 11, 8, 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, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 149, 149, 121, 107, 121, 74, 107, 34, 12, 32, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 149, 149, 107, 107, 107, 74, 74, 38, 38, 38, 38, 12, 12, 4, 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: 937
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071679 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071679
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071679/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071679
Building REAL250005071680
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071680'
/scratch/stefan/7916153/working/building/REAL250005071680 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071680

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071680/0 /scratch/stefan/7916153/working/building/REAL250005071680 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 817)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/817
`/scratch/stefan/7916153/working/3D/817' -> `0.mol2'
Preparing input files

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

`REAL250005071680.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071680.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071680/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071680 none C#CCCC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 1, 11, 8, 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, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 152, 125, 152, 95, 125, 46, 18, 45, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 200, 125, 125, 125, 95, 94, 49, 49, 49, 49, 18, 18, 4, 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: 871
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071680 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071680
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071680/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071680
Building REAL250005071681
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071681'
/scratch/stefan/7916153/working/building/REAL250005071681 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071681

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071681/0 /scratch/stefan/7916153/working/building/REAL250005071681 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 818)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/818
`/scratch/stefan/7916153/working/3D/818' -> `0.mol2'
Preparing input files

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

`REAL250005071681.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071681.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071681/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071681 none C=CC(O)C(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 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', '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: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 39, 43, 36, 39, 29, 36, 20, 12, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 129, 36, 36, 36, 29, 29, 20, 20, 20, 20, 12, 12, 5, 1] 129
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: 310
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071681 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071681
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071681/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071681
Building REAL250005071682
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071682'
/scratch/stefan/7916153/working/building/REAL250005071682 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071682

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071682/0 /scratch/stefan/7916153/working/building/REAL250005071682 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 819)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/819
`/scratch/stefan/7916153/working/3D/819' -> `0.mol2'
Preparing input files

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

`REAL250005071682.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071682.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071682/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071682 none CC(O)C(=O)N(C)CC(C)CNC(=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', 'C.3', '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, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens 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, 66, 67, 56, 66, 49, 56, 31, 13, 33, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 201, 56, 56, 56, 49, 49, 33, 33, 33, 33, 13, 13, 4, 1] 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])
total number of confs: 486
number of broken/clashed sets: 75
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071682 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071682
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071682/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071682
Building REAL250005071683
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071683'
/scratch/stefan/7916153/working/building/REAL250005071683 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071683

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071683/0 /scratch/stefan/7916153/working/building/REAL250005071683 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 820)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/820
`/scratch/stefan/7916153/working/3D/820' -> `0.mol2'
Preparing input files

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

`REAL250005071683.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071683.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071683/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071683 none CC(=O)C(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 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', '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, 1, 11, 8, 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, 6, 7]
dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 60, 81, 45, 60, 31, 45, 16, 10, 17, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 81, 81, 81, 45, 45, 45, 31, 31, 17, 17, 17, 17, 10, 10, 3, 1] 81
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])
total number of confs: 335
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071683 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071683
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071683/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071683
Building REAL250005071684
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071684'
/scratch/stefan/7916153/working/building/REAL250005071684 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071684

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071684/0 /scratch/stefan/7916153/working/building/REAL250005071684 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 821)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/821
`/scratch/stefan/7916153/working/3D/821' -> `0.mol2'
Preparing input files

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

`REAL250005071684.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071684.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071684/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071684 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1(F)CC1 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.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [39, 29, 39, 66, 79, 79, 79, 79, 79, 79, 79, 79, 12, 7, 12, 1, 7, 1, 1, 1, 1, 39, 39, 39, 39, 66, 66, 79, 79, 29, 29, 12, 12, 12, 1, 1, 1, 1] 79
rigid atoms, others: [34, 35, 36, 37, 15, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 347
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071684 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1(F)CC1 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.3', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [25, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 23, 37, 54, 54, 67, 67, 79, 79, 79, 25, 25, 25, 25, 12, 12, 4, 1, 37, 36, 54, 54, 54, 79, 79, 79, 79] 79
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 321
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071684 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071684
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071684/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071684
Building REAL250005071685
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071685'
/scratch/stefan/7916153/working/building/REAL250005071685 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071685

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071685/0 /scratch/stefan/7916153/working/building/REAL250005071685 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 822)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/822
`/scratch/stefan/7916153/working/3D/822' -> `0.mol2'
Preparing input files

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

`REAL250005071685.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071685.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071685/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071685 none CC=C(F)C(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 15, 1, 11, 8, 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, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 177, 201, 135, 177, 97, 135, 44, 16, 45, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 135, 135, 135, 97, 95, 49, 49, 49, 49, 16, 16, 4, 1] 201
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: 821
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071685 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071685
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071685/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071685
Building REAL250005071686
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071686'
/scratch/stefan/7916153/working/building/REAL250005071686 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071686

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071686/0 /scratch/stefan/7916153/working/building/REAL250005071686 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 823)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/823
`/scratch/stefan/7916153/working/3D/823' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C(C)CO)

`REAL250005071686.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071686.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071686/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071686 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C(C)CO 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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: [17, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 29, 42, 42, 48, 48, 51, 51, 51, 17, 17, 17, 17, 8, 8, 2, 1, 29, 29, 42, 42, 42, 51, 51, 51, 51, 51, 51, 153] 153
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 367
number of broken/clashed sets: 84
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071686 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071686
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071686/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071686
Building REAL250005071687
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071687'
/scratch/stefan/7916153/working/building/REAL250005071687 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071687

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071687/0 /scratch/stefan/7916153/working/building/REAL250005071687 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 824)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/824
`/scratch/stefan/7916153/working/3D/824' -> `0.mol2'
Preparing input files

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

`REAL250005071687.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071687.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071687/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071687 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1(O)CC1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [25, 21, 25, 44, 52, 52, 52, 52, 52, 52, 52, 52, 10, 6, 10, 1, 6, 1, 1, 1, 1, 25, 25, 25, 25, 44, 44, 52, 52, 21, 21, 10, 10, 10, 6, 1, 1, 1, 1] 156
rigid atoms, others: [35, 36, 37, 38, 15, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 220
number of broken/clashed sets: 58
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071687 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1(O)CC1 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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 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, 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
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [21, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 20, 31, 40, 40, 43, 43, 52, 52, 52, 21, 21, 21, 21, 10, 10, 3, 1, 31, 31, 40, 40, 40, 156, 52, 52, 52, 52] 156
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 369
number of broken/clashed sets: 58
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071687 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071687
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071687/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071687
Building REAL250005071688
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071688'
/scratch/stefan/7916153/working/building/REAL250005071688 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071688

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071688/0 /scratch/stefan/7916153/working/building/REAL250005071688 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 825)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/825
`/scratch/stefan/7916153/working/3D/825' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1=CCC1)

`REAL250005071688.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071688.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071688/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071688 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1=CCC1 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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 1, 1, 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, 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, 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: [15, 13, 15, 19, 20, 20, 20, 20, 20, 20, 20, 20, 8, 7, 8, 1, 7, 1, 1, 1, 1, 15, 15, 15, 15, 19, 19, 20, 20, 13, 13, 8, 8, 8, 1, 1, 1, 1, 1] 20
rigid atoms, others: [34, 35, 36, 37, 38, 15, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 86
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071688 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1=CCC1 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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 1, 1, 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, 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, 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, 6, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 13, 17, 17, 20, 20, 20, 20, 20, 11, 11, 11, 11, 6, 6, 2, 1, 13, 12, 17, 17, 17, 20, 20, 20, 20, 20] 20
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 87
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071688 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071688
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071688/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071688
Building REAL250005071689
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071689'
/scratch/stefan/7916153/working/building/REAL250005071689 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071689

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071689/0 /scratch/stefan/7916153/working/building/REAL250005071689 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 826)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/826
`/scratch/stefan/7916153/working/3D/826' -> `0.mol2'
Preparing input files

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

`REAL250005071689.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071689.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071689/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071689 none CC=CC(=O)N(C)CC(C)CNC(=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', 'C.3', '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, 1, 1, 1, 11, 8, 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, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 184, 148, 184, 105, 148, 54, 22, 55, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 148, 148, 148, 105, 103, 59, 59, 59, 59, 22, 22, 4, 1] 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])
total number of confs: 829
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071689 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071689
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071689/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071689
Building REAL250005071690
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071690'
/scratch/stefan/7916153/working/building/REAL250005071690 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071690

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071690/0 /scratch/stefan/7916153/working/building/REAL250005071690 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 827)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/827
`/scratch/stefan/7916153/working/3D/827' -> `0.mol2'
Preparing input files

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

`REAL250005071690.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071690.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071690/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071690 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C=CCF 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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [18, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 31, 48, 48, 65, 65, 81, 81, 81, 18, 18, 18, 18, 8, 8, 2, 1, 31, 30, 48, 48, 48, 81, 81, 81, 81] 81
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 322
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071690 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071690
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071690/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071690
Building REAL250005071691
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071691'
/scratch/stefan/7916153/working/building/REAL250005071691 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL250005071691 as failed and skipping
/scratch/stefan/7916153/working /scratch/stefan/7916153
`/scratch/stefan/7916153/working/building/REAL250005071691' -> `/scratch/stefan/7916153/failed/REAL250005071691'
Building REAL250005071692
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071692'
/scratch/stefan/7916153/working/building/REAL250005071692 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071692

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071692/0 /scratch/stefan/7916153/working/building/REAL250005071692 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 828)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/828
`/scratch/stefan/7916153/working/3D/828' -> `0.mol2'
Preparing input files

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

`REAL250005071692.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071692.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071692/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071692 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)[C@H](C)O 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.3', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 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
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [24, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 24, 39, 46, 46, 51, 51, 51, 51, 51, 25, 25, 25, 25, 13, 13, 4, 1, 39, 39, 46, 46, 46, 51, 51, 51, 153] 153
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 375
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071692 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071692
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071692/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071692
Building REAL250005071693
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071693'
/scratch/stefan/7916153/working/building/REAL250005071693 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071693

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071693/0 /scratch/stefan/7916153/working/building/REAL250005071693 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 829)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/829
`/scratch/stefan/7916153/working/3D/829' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=CC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005071693.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071693.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071693/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071693 none CON=CC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 12, 8, 1, 1, 11, 8, 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, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 94, 87, 94, 73, 87, 39, 17, 43, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 87, 87, 87, 73, 73, 43, 43, 43, 43, 17, 17, 5, 1] 154
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: 614
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071693 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071693
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071693/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071693
Building REAL250005071694
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071694'
/scratch/stefan/7916153/working/building/REAL250005071694 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071694

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071694/0 /scratch/stefan/7916153/working/building/REAL250005071694 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 830)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/830
`/scratch/stefan/7916153/working/3D/830' -> `0.mol2'
Preparing input files

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

`REAL250005071694.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071694.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071694/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071694 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)[C@@H]1C[C@H]1C 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.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 7, 5, 5, 7, 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, 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, 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: [40, 30, 40, 75, 95, 95, 95, 95, 95, 95, 95, 95, 12, 7, 12, 1, 7, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 75, 75, 95, 95, 30, 30, 12, 12, 12, 1, 1, 2, 2, 2] 95
rigid atoms, others: [36, 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, 38, 39, 40])
total number of confs: 415
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071694 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)[C@@H]1C[C@H]1C 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.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 7, 5, 5, 7, 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, 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, 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: [28, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 38, 54, 54, 65, 65, 95, 95, 95, 95, 95, 28, 28, 28, 28, 11, 11, 2, 1, 38, 38, 54, 54, 54, 95, 95, 95, 95, 95] 95
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 387
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071694 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071694
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071694/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071694
Building REAL250005071695
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071695'
/scratch/stefan/7916153/working/building/REAL250005071695 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071695

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071695/0 /scratch/stefan/7916153/working/building/REAL250005071695 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 831)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/831
`/scratch/stefan/7916153/working/3D/831' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C(C)(C)O)

`REAL250005071695.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071695.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071695/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071695 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C(C)(C)O 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 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: [21, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 20, 31, 34, 34, 34, 34, 42, 42, 42, 21, 21, 21, 21, 9, 9, 3, 1, 31, 31, 34, 34, 34, 42, 42, 42, 42, 42, 42, 126] 126
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 322
number of broken/clashed sets: 81
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071695 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071695
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071695/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071695
Building REAL250005071696
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071696'
/scratch/stefan/7916153/working/building/REAL250005071696 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071696

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071696/0 /scratch/stefan/7916153/working/building/REAL250005071696 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 832)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/832
`/scratch/stefan/7916153/working/3D/832' -> `0.mol2'
Preparing input files

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

`REAL250005071696.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071696.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071696/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071696 none C=C(C)CC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 115, 96, 115, 73, 96, 35, 13, 35, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 96, 96, 96, 73, 73, 39, 39, 39, 39, 13, 13, 4, 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: 900
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071696 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071696
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071696/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071696
Building REAL250005071697
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071697'
/scratch/stefan/7916153/working/building/REAL250005071697 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071697

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071697/0 /scratch/stefan/7916153/working/building/REAL250005071697 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 833)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/833
`/scratch/stefan/7916153/working/3D/833' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005071697.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071697.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071697/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071697 none C=CCC(=O)N(C)CC(C)CNC(=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', 'C.3', '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: [1, 1, 5, 1, 11, 8, 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, 6, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 132, 110, 132, 81, 110, 42, 16, 41, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 110, 110, 110, 81, 81, 46, 46, 46, 46, 16, 16, 4, 1] 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])
total number of confs: 921
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071697 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071697
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071697/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071697
Building REAL250005071698
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071698'
/scratch/stefan/7916153/working/building/REAL250005071698 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071698

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071698/0 /scratch/stefan/7916153/working/building/REAL250005071698 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 834)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/834
`/scratch/stefan/7916153/working/3D/834' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C[NH+](C)C)

`REAL250005071698.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071698.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071698/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071698 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C[NH+](C)C 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.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [18, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 17, 20, 21, 21, 21, 21, 21, 21, 21, 21, 18, 18, 18, 18, 13, 13, 4, 1, 20, 20, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 21
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 29] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 94
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071698 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071698/1 /scratch/stefan/7916153/working/building/REAL250005071698 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 835)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/835
`/scratch/stefan/7916153/working/3D/835' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)CN(C)C)

`REAL250005071698.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071698.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071698/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.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: REAL250005071698 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)CN(C)C 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.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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, 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: [22, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 21, 38, 48, 48, 64, 64, 71, 72, 72, 22, 22, 22, 22, 10, 10, 3, 1, 38, 37, 48, 48, 48, 71, 71, 72, 72, 72, 72, 72, 72] 72
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 305
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071698 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071698
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071698/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071698/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071698
Building REAL250005071699
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071699'
/scratch/stefan/7916153/working/building/REAL250005071699 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071699

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071699/0 /scratch/stefan/7916153/working/building/REAL250005071699 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 836)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/836
`/scratch/stefan/7916153/working/3D/836' -> `0.mol2'
Preparing input files

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

`REAL250005071699.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071699.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071699/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071699 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)CC#N 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.3', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 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
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [43, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 71, 98, 98, 124, 124, 155, 155, 45, 45, 45, 45, 16, 16, 4, 1, 71, 69, 98, 98, 98, 155, 155] 155
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])
total number of confs: 671
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071699 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071699
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071699/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071699
Building REAL250005071700
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071700'
/scratch/stefan/7916153/working/building/REAL250005071700 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071700

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071700/0 /scratch/stefan/7916153/working/building/REAL250005071700 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 837)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/837
`/scratch/stefan/7916153/working/3D/837' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1CC1F)

`REAL250005071700.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071700.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071700/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071700 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1CC1F 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [41, 31, 41, 79, 97, 97, 97, 97, 97, 97, 97, 97, 12, 5, 12, 1, 5, 1, 1, 1, 1, 41, 41, 41, 41, 79, 79, 97, 97, 31, 31, 12, 12, 12, 1, 1, 1, 1] 97
rigid atoms, others: [34, 35, 36, 37, 15, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 416
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071700 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)C1CC1F 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [28, 11, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 26, 38, 52, 52, 66, 66, 97, 97, 97, 28, 28, 28, 28, 11, 11, 4, 1, 38, 38, 52, 52, 52, 97, 97, 97, 97] 97
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 400
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071700 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071700
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071700/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071700
Building REAL250005071701
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071701'
/scratch/stefan/7916153/working/building/REAL250005071701 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071701

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071701/0 /scratch/stefan/7916153/working/building/REAL250005071701 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 838)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/838
`/scratch/stefan/7916153/working/3D/838' -> `0.mol2'
Preparing input files

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

`REAL250005071701.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071701.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071701/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071701 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)CCF 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.3', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [27, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 25, 47, 68, 68, 86, 86, 110, 110, 27, 27, 27, 27, 13, 13, 4, 1, 47, 46, 68, 68, 68, 110, 110, 110, 110] 110
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: 463
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071701 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071701
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071701/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071701
Building REAL250005071702
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071702'
/scratch/stefan/7916153/working/building/REAL250005071702 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071702

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071702/0 /scratch/stefan/7916153/working/building/REAL250005071702 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 839)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/839
`/scratch/stefan/7916153/working/3D/839' -> `0.mol2'
Preparing input files

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

`REAL250005071702.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071702.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071702/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071702 none CO[C@H](C)C(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 12, 5, 7, 5, 1, 11, 8, 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, 6, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 196, 196, 140, 161, 105, 140, 61, 26, 61, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 196, 196, 196, 140, 140, 140, 105, 102, 66, 66, 66, 66, 26, 26, 5, 1] 201
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: 907
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071702 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071702
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071702/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071702
Building REAL250005071703
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071703'
/scratch/stefan/7916153/working/building/REAL250005071703 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071703

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071703/0 /scratch/stefan/7916153/working/building/REAL250005071703 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 840)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/840
`/scratch/stefan/7916153/working/3D/840' -> `0.mol2'
Preparing input files

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

`REAL250005071703.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071703.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071703/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071703 none CC(CNC(=O)C1=CC(=O)[N-]O1)CN(C)C(=O)[C@@H](C)O 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.3', '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', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 5, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 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
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [24, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 24, 39, 47, 47, 51, 51, 51, 51, 51, 25, 25, 25, 25, 13, 13, 4, 1, 39, 39, 47, 47, 47, 51, 51, 51, 153] 153
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 375
number of broken/clashed sets: 57
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071703 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071703
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071703/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071703
Building REAL250005071704
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071704'
/scratch/stefan/7916153/working/building/REAL250005071704 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071704

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071704/0 /scratch/stefan/7916153/working/building/REAL250005071704 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 841)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/841
`/scratch/stefan/7916153/working/3D/841' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005071704.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071704.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071704/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071704 none C=C1CC1C(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 1, 11, 8, 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, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 145, 117, 145, 88, 117, 44, 17, 43, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 117, 117, 117, 87, 88, 48, 48, 48, 48, 17, 17, 4, 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: 820
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071704 none C=C1CC1C(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 1, 11, 8, 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, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 16, 16, 40, 61, 61, 117, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 16, 16, 16, 40, 40, 61, 61, 61, 61, 117, 117, 201, 201] 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, 37, 38])
total number of confs: 793
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071704 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071704
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071704/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071704
Building REAL250005071705
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071705'
/scratch/stefan/7916153/working/building/REAL250005071705 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071705

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071705/0 /scratch/stefan/7916153/working/building/REAL250005071705 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 842)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/842
`/scratch/stefan/7916153/working/3D/842' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005071705.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071705.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071705/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071705 none CC1=CC1C(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 1, 5, 1, 11, 8, 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, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 149, 115, 149, 85, 115, 41, 14, 42, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 115, 115, 115, 85, 84, 45, 45, 45, 45, 14, 14, 4, 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: 808
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071705 none CC1=CC1C(=O)N(C)CC(C)CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 1, 5, 1, 11, 8, 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, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 17, 17, 41, 64, 64, 125, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 17, 17, 17, 41, 41, 64, 64, 64, 64, 125, 125, 201, 201] 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, 37, 38])
total number of confs: 813
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071705 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071705
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071705/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071705
Building REAL250005071706
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071706'
/scratch/stefan/7916153/working/building/REAL250005071706 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071706

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071706/0 /scratch/stefan/7916153/working/building/REAL250005071706 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 843)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/843
`/scratch/stefan/7916153/working/3D/843' -> `0.mol2'
Preparing input files

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

`REAL250005071706.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071706.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071706/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.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: REAL250005071706 none C=CC(=O)N(C)CC(C)CNC(=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', '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, 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, 6, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 54, 66, 33, 54, 17, 9, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 66, 66, 66, 54, 54, 54, 33, 33, 19, 19, 19, 19, 9, 9, 2, 1] 66
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])
total number of confs: 270
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071706 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071706
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071706/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071706
Building REAL250005071707
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071707'
/scratch/stefan/7916153/working/building/REAL250005071707 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071707

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071707/0 /scratch/stefan/7916153/working/building/REAL250005071707 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 844)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/844
`/scratch/stefan/7916153/working/3D/844' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N(C)CC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071707.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071707.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071707/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071707 none CCC(=O)N(C)CC1CCN(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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 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, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 191, 145, 191, 91, 145, 27, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 201, 201, 201, 201, 201, 145, 145, 145, 91, 91, 27, 27, 27, 27, 27, 1, 27, 27, 27, 27] 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: 715
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071707 none CCC(=O)N(C)CC1CCN(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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 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, 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, 7, 7]
0  hydrogens 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, 54, 27, 54, 10, 27, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 82, 82, 82, 82, 82, 27, 27, 27, 10, 10, 1, 1, 1, 1, 1, 27, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 37, 6, 7, 8, 9, 10, 11, 40, 19, 20, 39, 38, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36])
total number of confs: 326
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071707 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071707
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071707/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071707
Building REAL250005071708
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071708'
/scratch/stefan/7916153/working/building/REAL250005071708 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071708

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071708/0 /scratch/stefan/7916153/working/building/REAL250005071708 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 845)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/845
`/scratch/stefan/7916153/working/3D/845' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N(C)CC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071708.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071708.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071708/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071708 none CC(=O)N(C)CC1CCN(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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 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, 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
122  conformations in input
total number of sets (complete confs): 122
using faster count positions algorithm for large data
unique positions, atoms: [122, 119, 122, 96, 119, 34, 34, 34, 34, 12, 1, 12, 1, 1, 1, 1, 1, 1, 34, 34, 122, 122, 122, 119, 119, 119, 96, 96, 34, 34, 34, 34, 34, 1, 34, 34, 34, 34] 122
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: 423
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071708 none CC(=O)N(C)CC1CCN(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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 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, 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
122  conformations in input
total number of sets (complete confs): 122
using faster count positions algorithm for large data
unique positions, atoms: [33, 17, 33, 8, 17, 1, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 34, 1, 1, 33, 33, 33, 17, 17, 17, 8, 8, 1, 1, 1, 1, 1, 34, 1, 1, 1, 1] 122
rigid atoms, others: [32, 34, 35, 36, 5, 6, 7, 8, 9, 10, 18, 19, 37, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 33, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 148
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071708 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071708
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071708/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071708
Building REAL250005071709
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071709'
/scratch/stefan/7916153/working/building/REAL250005071709 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071709

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071709/0 /scratch/stefan/7916153/working/building/REAL250005071709 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 846)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/846
`/scratch/stefan/7916153/working/3D/846' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)C(=O)CO)

`REAL250005071709.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071709.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071709/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071709 none CN(CC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)C(=O)CO NO_LONG_NAME
dock atom types: ['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', 'C.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']
dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [122, 57, 19, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 122, 186, 186, 201, 122, 122, 122, 57, 57, 19, 19, 19, 19, 19, 1, 19, 19, 19, 19, 201, 201, 603] 603
rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 1335
number of broken/clashed sets: 221
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071709 none CN(CC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)C(=O)CO NO_LONG_NAME
dock atom types: ['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', 'C.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']
dock atom type numbers: [5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 13, 37, 37, 95, 13, 13, 13, 5, 5, 1, 1, 1, 1, 1, 19, 1, 1, 1, 1, 95, 95, 285] 603
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 15, 16, 35, 26, 27, 28, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 36, 37, 38])
total number of confs: 693
number of broken/clashed sets: 221
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071709 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071709
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071709/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071709
Building REAL250005071710
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071710'
/scratch/stefan/7916153/working/building/REAL250005071710 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071710

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071710/0 /scratch/stefan/7916153/working/building/REAL250005071710 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 847)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/847
`/scratch/stefan/7916153/working/3D/847' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1CCC(CN(C)C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071710.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071710.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071710/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071710 none CCC(=O)N1CCC(CN(C)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', 'C.3', 'C.3', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 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, 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, 7, 7]
0  hydrogens need rotated
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, 201, 114, 114, 114, 85, 36, 11, 36, 1, 11, 1, 1, 1, 1, 1, 1, 114, 114, 201, 201, 201, 201, 201, 114, 114, 114, 114, 114, 85, 85, 36, 36, 36, 1, 114, 114, 114, 114] 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: 680
number of broken/clashed sets: 49
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071710 none CCC(=O)N1CCC(CN(C)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', 'C.3', 'C.3', 'N.am', 'C.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', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 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, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 6, 1, 6, 1, 1, 1, 1, 1, 7, 19, 19, 67, 67, 114, 114, 114, 114, 114, 1, 1, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 114, 1, 1, 1, 1] 201
rigid atoms, others: [2, 4, 5, 6, 7, 8, 38, 39, 40, 19, 20, 26, 27, 28, 29, 30, 37] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36])
total number of confs: 327
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071710 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071710
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071710/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071710
Building REAL250005071711
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071711'
/scratch/stefan/7916153/working/building/REAL250005071711 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071711

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071711/0 /scratch/stefan/7916153/working/building/REAL250005071711 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 848)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/848
`/scratch/stefan/7916153/working/3D/848' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCC(CN(C)C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071711.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071711.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071711/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071711 none CC(=O)N1CCC(CN(C)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', 'C.3', 'N.am', 'C.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, 5, 8, 5, 1, 11, 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, 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
198  conformations in input
total number of sets (complete confs): 198
using faster count positions algorithm for large data
unique positions, atoms: [198, 137, 198, 137, 137, 137, 101, 42, 12, 42, 1, 12, 1, 1, 1, 1, 1, 1, 137, 137, 198, 198, 198, 137, 137, 137, 137, 137, 101, 101, 42, 42, 42, 1, 137, 137, 137, 137] 198
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: 727
number of broken/clashed sets: 92
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071711 none CC(=O)N1CCC(CN(C)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', 'C.3', 'N.am', 'C.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, 5, 8, 5, 1, 11, 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, 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
198  conformations in input
total number of sets (complete confs): 198
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 9, 24, 24, 73, 73, 137, 137, 137, 137, 137, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 24, 24, 24, 137, 1, 1, 1, 1] 198
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 18, 19, 23, 24, 25, 26, 27, 36, 37, 35] set([0, 32, 2, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 28, 29, 30, 31])
total number of confs: 312
number of broken/clashed sets: 92
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071711 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071711
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071711/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071711
Building REAL250005071712
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071712'
/scratch/stefan/7916153/working/building/REAL250005071712 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071712

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071712/0 /scratch/stefan/7916153/working/building/REAL250005071712 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 849)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/849
`/scratch/stefan/7916153/working/3D/849' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CC1CCN(C(=O)CO)CC1)C(=O)C1=CC(=O)[N-]O1)

`REAL250005071712.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071712.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071712/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071712 none CN(CC1CCN(C(=O)CO)CC1)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 6, 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: [31, 10, 31, 76, 121, 121, 121, 121, 199, 199, 201, 121, 121, 1, 10, 1, 1, 1, 1, 1, 1, 31, 31, 31, 76, 76, 121, 121, 121, 121, 121, 201, 201, 603, 121, 121, 121, 121, 1] 603
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: 1307
number of broken/clashed sets: 196
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071712 none CN(CC1CCN(C(=O)CO)CC1)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 6, 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: [19, 7, 1, 1, 1, 1, 1, 1, 6, 6, 20, 1, 1, 19, 65, 65, 121, 121, 121, 121, 121, 19, 19, 19, 7, 7, 1, 1, 1, 1, 1, 20, 20, 60, 1, 1, 1, 1, 121] 603
rigid atoms, others: [2, 3, 4, 5, 6, 7, 11, 12, 34, 35, 36, 26, 27, 28, 29, 30, 37] set([0, 1, 8, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 38])
total number of confs: 409
number of broken/clashed sets: 196
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071712 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071712
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071712/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071712
Building REAL250005071713
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071713'
/scratch/stefan/7916153/working/building/REAL250005071713 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071713

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071713/0 /scratch/stefan/7916153/working/building/REAL250005071713 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 850)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/850
`/scratch/stefan/7916153/working/3D/850' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N1CCC(CN(C)C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071713.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071713.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071713/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071713 none C=CC(=O)N1CCC(CN(C)C(=O)C2=CC(=O)[N-]O2)CC1 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.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: [1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 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, 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
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, 201, 113, 113, 113, 75, 33, 10, 33, 1, 10, 1, 1, 1, 1, 1, 1, 113, 113, 201, 201, 201, 113, 113, 113, 113, 113, 75, 75, 33, 33, 33, 1, 113, 113, 113, 113] 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: 705
number of broken/clashed sets: 44
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071713 none C=CC(=O)N1CCC(CN(C)C(=O)C2=CC(=O)[N-]O2)CC1 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.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: [1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 5, 1, 11, 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, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 7, 1, 7, 1, 1, 1, 1, 1, 7, 17, 17, 62, 62, 113, 113, 113, 113, 113, 1, 1, 24, 24, 24, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 113, 1, 1, 1, 1] 201
rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 38, 19, 20, 24, 25, 26, 27, 28, 37, 36] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 29, 30, 31, 32, 33, 34])
total number of confs: 312
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071713 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071713
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071713/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071713
Building REAL250005071714
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071714'
/scratch/stefan/7916153/working/building/REAL250005071714 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071714

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071714/0 /scratch/stefan/7916153/working/building/REAL250005071714 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 851)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/851
`/scratch/stefan/7916153/working/3D/851' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC1CC2(C1)CCN(C(=O)C1=CC(=O)[N-]O1)CC2)

`REAL250005071714.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071714.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071714/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071714 none CC(=O)NC1CC2(C1)CCN(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 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, 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, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 27, 19, 19, 19, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 27, 27, 27, 27, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 19, 19, 19, 19] 27
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: 67
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071714 none CC(=O)NC1CC2(C1)CCN(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 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, 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, 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: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 1, 1, 1, 1] 27
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38] set([0, 1, 2, 34, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24])
total number of confs: 45
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071714 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071714
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071714/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071714
Building REAL250005071715
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071715'
/scratch/stefan/7916153/working/building/REAL250005071715 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071715

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071715/0 /scratch/stefan/7916153/working/building/REAL250005071715 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 852)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/852
`/scratch/stefan/7916153/working/3D/852' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCC2(CC(NC(=O)C3=CC(=O)[N-]O3)C2)CC1)

`REAL250005071715.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071715.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071715/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071715 none CC(=O)N1CCC2(CC(NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 4, 7, 6, 7, 7, 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
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [24, 13, 24, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 24, 24, 24, 13, 13, 13, 13, 13, 13, 13, 4, 1, 13, 13, 13, 13, 13, 13] 24
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: 79
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071715 none CC(=O)N1CCC2(CC(NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 4, 7, 6, 7, 7, 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
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 13, 1, 1, 1, 1, 1, 1] 24
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38] set([0, 32, 2, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 31])
total number of confs: 32
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071715 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071715
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071715/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071715
Building REAL250005071716
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071716'
/scratch/stefan/7916153/working/building/REAL250005071716 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071716

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071716/0 /scratch/stefan/7916153/working/building/REAL250005071716 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 853)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/853
`/scratch/stefan/7916153/working/3D/853' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071716.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071716.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071716/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071716 none CCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 29, 18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 29, 29, 29, 29, 29, 18, 18, 18, 18, 18, 18, 1, 18, 18, 18, 18] 29
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: 72
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071716 none CCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 1, 1, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 18, 1, 1, 1, 1] 29
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 17, 18, 24, 25, 26, 27, 28, 29, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 30])
total number of confs: 60
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071716 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071716
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071716/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071716
Building REAL250005071717
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071717'
/scratch/stefan/7916153/working/building/REAL250005071717 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071717

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071717/0 /scratch/stefan/7916153/working/building/REAL250005071717 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 854)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/854
`/scratch/stefan/7916153/working/3D/854' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071717.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071717.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071717/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071717 none COCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 78, 50, 25, 50, 25, 25, 25, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 90, 90, 90, 90, 90, 78, 78, 25, 25, 25, 25, 25, 25, 1, 25, 25, 25, 25] 90
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: 320
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071717 none COCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 23, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 41, 41, 41, 23, 23, 15, 15, 1, 1, 1, 1, 1, 1, 25, 1, 1, 1, 1] 90
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 158
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071717 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071717
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071717/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071717
Building REAL250005071718
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071718'
/scratch/stefan/7916153/working/building/REAL250005071718 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071718

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071718/0 /scratch/stefan/7916153/working/building/REAL250005071718 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 855)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/855
`/scratch/stefan/7916153/working/3D/855' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071718.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071718.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071718/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071718 none CC(=O)N1CCCN(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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 11, 8, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 19, 28, 19, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 28, 28, 28, 19, 19, 19, 19, 19, 19, 1, 19, 19, 19, 19] 28
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: 70
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071718 none CC(=O)N1CCCN(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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 11, 8, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 19, 1, 1, 1, 1] 28
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 16, 17, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 27])
total number of confs: 44
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071718 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071718
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071718/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071718
Building REAL250005071719
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071719'
/scratch/stefan/7916153/working/building/REAL250005071719 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071719

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071719/0 /scratch/stefan/7916153/working/building/REAL250005071719 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 856)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/856
`/scratch/stefan/7916153/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)N1CCCN(C(=O)C2CC2)CC1)

`REAL250005071719.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071719.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071719/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071719 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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: [7, 1, 7, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 1, 1, 13, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 1, 1] 34
rigid atoms, others: [32, 1, 34, 35, 33, 8, 9, 10, 11, 12, 13, 18, 19, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 27, 28, 29, 30, 31])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071719 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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: [8, 1, 1, 1, 1, 1, 1, 1, 8, 13, 13, 13, 13, 13, 20, 20, 34, 34, 13, 13, 1, 13, 13, 13, 13, 13, 13, 34, 34, 34, 34, 34, 13, 13, 13, 13] 34
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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071719 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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: [24, 8, 24, 34, 34, 34, 34, 34, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 8, 8, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8] 34
rigid atoms, others: [13, 15, 16, 17, 27, 28, 29, 30, 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, 32, 33, 34, 35])
total number of confs: 79
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071719 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071719
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071719/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071719
Building REAL250005071720
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071720'
/scratch/stefan/7916153/working/building/REAL250005071720 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071720

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071720/0 /scratch/stefan/7916153/working/building/REAL250005071720 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 857)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/857
`/scratch/stefan/7916153/working/3D/857' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCCN(C(=O)C2CCC2)CC1)

`REAL250005071720.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071720.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071720/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071720 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 1, 1, 27, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1] 65
rigid atoms, others: [1, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 3, 4, 5, 6, 7, 34, 14, 15, 16, 17, 18, 21, 33, 28, 29, 30, 31])
total number of confs: 93
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071720 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 1, 10, 27, 27, 27, 27, 27, 54, 54, 65, 65, 65, 27, 27, 1, 27, 27, 27, 27, 27, 27, 65, 65, 65, 65, 65, 65, 65, 27, 27, 27, 27] 65
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: 174
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071720 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [53, 20, 53, 65, 65, 65, 65, 65, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 20, 20, 65, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20] 65
rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38])
total number of confs: 152
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071720 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071720
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071720/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071720
Building REAL250005071721
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071721'
/scratch/stefan/7916153/working/building/REAL250005071721 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071721

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071721/0 /scratch/stefan/7916153/working/building/REAL250005071721 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 858)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/858
`/scratch/stefan/7916153/working/3D/858' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC1)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071721.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071721.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071721/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071721 none O=C(CC1CC1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 8, 5, 5, 5, 8, 1, 11, 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
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 23, 33, 33, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 23, 23, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 124
rigid atoms, others: [32, 1, 35, 36, 33, 6, 7, 8, 9, 10, 11, 37, 19, 20, 38, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 162
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071721 none O=C(CC1CC1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 8, 5, 5, 5, 8, 1, 11, 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
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [14, 3, 1, 1, 1, 1, 14, 33, 33, 33, 33, 33, 87, 87, 124, 124, 124, 124, 124, 33, 33, 3, 3, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 124, 33, 33, 33, 33] 124
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: 285
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071721 none O=C(CC1CC1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 8, 5, 5, 5, 8, 1, 11, 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
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [79, 29, 79, 99, 124, 124, 29, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 99, 99, 124, 124, 124, 124, 124, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 124
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: 410
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071721 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071721
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071721/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071721
Building REAL250005071722
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071722'
/scratch/stefan/7916153/working/building/REAL250005071722 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071722

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071722/0 /scratch/stefan/7916153/working/building/REAL250005071722 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 859)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/859
`/scratch/stefan/7916153/working/3D/859' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(F)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071722.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071722.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071722/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071722 none CC(C)(F)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 39, 45, 45, 22, 39, 22, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 45, 45, 45, 45, 45, 45, 22, 22, 22, 22, 22, 22, 1, 22, 22, 22, 22] 45
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: 130
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071722 none CC(C)(F)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [9, 6, 9, 9, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 22, 1, 1, 1, 1] 45
rigid atoms, others: [32, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 33, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26])
total number of confs: 66
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071722 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071722
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071722/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071722
Building REAL250005071723
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071723'
/scratch/stefan/7916153/working/building/REAL250005071723 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071723

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071723/0 /scratch/stefan/7916153/working/building/REAL250005071723 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 860)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/860
`/scratch/stefan/7916153/working/3D/860' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071723.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071723.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071723/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071723 none COCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 61, 29, 61, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 97, 97, 97, 96, 96, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 97
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: 334
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071723 none COCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 34, 34, 34, 16, 16, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 97
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 29, 30, 35] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31])
total number of confs: 132
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071723 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071723
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071723/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071723
Building REAL250005071724
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071724'
/scratch/stefan/7916153/working/building/REAL250005071724 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071724

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071724/0 /scratch/stefan/7916153/working/building/REAL250005071724 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 861)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/861
`/scratch/stefan/7916153/working/3D/861' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071724.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071724.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071724/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071724 none CCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 50, 25, 50, 25, 25, 25, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 85, 85, 85, 85, 85, 85, 85, 25, 25, 25, 25, 25, 25, 1, 25, 25, 25, 25] 85
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: 291
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071724 none CCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [24, 18, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 26, 26, 26, 25, 25, 18, 18, 1, 1, 1, 1, 1, 1, 25, 1, 1, 1, 1] 85
rigid atoms, others: [32, 35, 34, 3, 36, 5, 6, 7, 8, 9, 10, 37, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 33, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 157
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071724 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071724
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071724/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071724
Building REAL250005071725
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071725'
/scratch/stefan/7916153/working/building/REAL250005071725 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071725

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071725/0 /scratch/stefan/7916153/working/building/REAL250005071725 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 862)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/862
`/scratch/stefan/7916153/working/3D/862' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071725.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071725.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071725/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071725 none CC(C)CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 38, 18, 38, 18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 52, 52, 52, 52, 52, 52, 52, 52, 52, 18, 18, 18, 18, 18, 18, 1, 18, 18, 18, 18] 52
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: 172
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071725 none CC(C)CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [13, 11, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 1, 1, 13, 13, 13, 13, 13, 13, 13, 11, 11, 1, 1, 1, 1, 1, 1, 18, 1, 1, 1, 1] 52
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 19, 20, 39, 38, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 77
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071725 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071725
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071725/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071725
Building REAL250005071726
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071726'
/scratch/stefan/7916153/working/building/REAL250005071726 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071726

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071726/0 /scratch/stefan/7916153/working/building/REAL250005071726 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 863)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/863
`/scratch/stefan/7916153/working/3D/863' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071726.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071726.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071726/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071726 none CC1CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 23, 1, 1, 1, 1] 67
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 93
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071726 none CC1CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 54, 54, 67, 67, 67, 67, 67, 22, 22, 2, 2, 2, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 67, 22, 22, 22, 22] 67
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: 157
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071726 none CC1CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 51, 23, 51, 23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 67, 67, 67, 67, 67, 67, 67, 23, 23, 23, 23, 23, 23, 1, 23, 23, 23, 23] 67
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: 191
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071726 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071726
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071726/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071726
Building REAL250005071727
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071727'
/scratch/stefan/7916153/working/building/REAL250005071727 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071727

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071727/0 /scratch/stefan/7916153/working/building/REAL250005071727 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 864)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/864
`/scratch/stefan/7916153/working/3D/864' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071727.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071727.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071727/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071727 none CCOCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 167, 136, 73, 28, 73, 28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 168, 168, 168, 168, 168, 136, 136, 28, 28, 28, 28, 28, 28, 1, 28, 28, 28, 28] 168
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: 545
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071727 none CCOCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [64, 55, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 65, 65, 65, 64, 64, 22, 22, 1, 1, 1, 1, 1, 1, 28, 1, 1, 1, 1] 168
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 226
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071727 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071727
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071727/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071727
Building REAL250005071728
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071728'
/scratch/stefan/7916153/working/building/REAL250005071728 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071728

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071728/0 /scratch/stefan/7916153/working/building/REAL250005071728 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 865)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/865
`/scratch/stefan/7916153/working/3D/865' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071728.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071728.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071728/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071728 none CC(C)=CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 48, 25, 48, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 67, 67, 67, 67, 67, 67, 67, 25, 25, 25, 25, 25, 25, 1, 25, 25, 25, 25] 67
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: 194
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071728 none CC(C)=CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 25, 1, 1, 1, 1] 67
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 89
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071728 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071728
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071728/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071728
Building REAL250005071729
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071729'
/scratch/stefan/7916153/working/building/REAL250005071729 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071729

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071729/0 /scratch/stefan/7916153/working/building/REAL250005071729 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 866)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/866
`/scratch/stefan/7916153/working/3D/866' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071729.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071729.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071729/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071729 none CSCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 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
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [137, 108, 73, 30, 73, 30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 137, 137, 137, 108, 108, 30, 30, 30, 30, 30, 30, 1, 30, 30, 30, 30] 137
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: 410
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071729 none CSCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 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
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [52, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 52, 52, 52, 22, 22, 1, 1, 1, 1, 1, 1, 30, 1, 1, 1, 1] 137
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 29, 30, 35] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31])
total number of confs: 167
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071729 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071729
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071729/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071729
Building REAL250005071730
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071730'
/scratch/stefan/7916153/working/building/REAL250005071730 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071730

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071730/0 /scratch/stefan/7916153/working/building/REAL250005071730 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 867)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/867
`/scratch/stefan/7916153/working/3D/867' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071730.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071730.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071730/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071730 none CCCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [99, 96, 87, 52, 24, 52, 24, 24, 24, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 99, 99, 99, 99, 99, 96, 96, 87, 87, 24, 24, 24, 24, 24, 24, 1, 24, 24, 24, 24] 99
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: 369
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071730 none CCCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 23, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 34, 34, 34, 33, 33, 24, 24, 15, 15, 1, 1, 1, 1, 1, 1, 24, 1, 1, 1, 1] 99
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 19, 20, 39, 38, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 198
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071730 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071730
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071730/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071730
Building REAL250005071731
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071731'
/scratch/stefan/7916153/working/building/REAL250005071731 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071731

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071731/0 /scratch/stefan/7916153/working/building/REAL250005071731 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 868)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/868
`/scratch/stefan/7916153/working/3D/868' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071731.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071731.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071731/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071731 none CC(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 20, 39, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 20, 20, 1, 20, 20, 20, 20] 39
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: 96
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071731 none CC(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [9, 6, 9, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 20, 1, 1, 1, 1] 39
rigid atoms, others: [32, 35, 34, 3, 36, 5, 6, 7, 8, 9, 10, 37, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 33, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 64
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071731 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071731
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071731/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071731
Building REAL250005071732
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071732'
/scratch/stefan/7916153/working/building/REAL250005071732 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071732

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071732/0 /scratch/stefan/7916153/working/building/REAL250005071732 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 869)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/869
`/scratch/stefan/7916153/working/3D/869' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071732.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071732.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071732/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071732 none CCC(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 77, 64, 77, 26, 64, 26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 81, 81, 81, 81, 81, 77, 77, 77, 77, 26, 26, 26, 26, 26, 26, 1, 26, 26, 26, 26] 81
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: 251
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071732 none CCC(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 20, 20, 20, 20, 20, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 26, 1, 1, 1, 1] 81
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 19, 20, 39, 38, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 133
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071732 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071732
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071732/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071732
Building REAL250005071733
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071733'
/scratch/stefan/7916153/working/building/REAL250005071733 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071733

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071733/0 /scratch/stefan/7916153/working/building/REAL250005071733 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 870)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/870
`/scratch/stefan/7916153/working/3D/870' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071733.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071733.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071733/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071733 none COC(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 45, 36, 45, 20, 36, 20, 20, 20, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 47, 47, 47, 45, 45, 45, 45, 20, 20, 20, 20, 20, 20, 1, 20, 20, 20, 20] 47
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: 143
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071733 none COC(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 12, 5, 12, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 21, 21, 21, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 20, 1, 1, 1, 1] 47
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 92
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071733 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071733
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071733/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071733
Building REAL250005071734
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071734'
/scratch/stefan/7916153/working/building/REAL250005071734 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071734

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071734/0 /scratch/stefan/7916153/working/building/REAL250005071734 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 871)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/871
`/scratch/stefan/7916153/working/3D/871' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071734.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071734.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071734/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071734 none C=CCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [105, 105, 89, 49, 27, 49, 27, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 105, 105, 105, 105, 105, 89, 89, 27, 27, 27, 27, 27, 27, 1, 27, 27, 27, 27] 105
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: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071734 none C=CCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [44, 26, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 44, 44, 44, 26, 26, 15, 15, 1, 1, 1, 1, 1, 1, 27, 1, 1, 1, 1] 105
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 214
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071734 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071734
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071734/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071734
Building REAL250005071735
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071735'
/scratch/stefan/7916153/working/building/REAL250005071735 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071735

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071735/0 /scratch/stefan/7916153/working/building/REAL250005071735 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 872)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/872
`/scratch/stefan/7916153/working/3D/872' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(C)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071735.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071735.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071735/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071735 none CC=C(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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, 56, 36, 56, 21, 36, 21, 21, 21, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 21, 56, 56, 56, 56, 56, 56, 56, 21, 21, 21, 21, 21, 21, 1, 21, 21, 21, 21] 56
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: 174
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071735 none CC=C(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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: [14, 14, 7, 14, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 21, 1, 1, 1, 1] 56
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 74
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071735 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071735
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071735/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071735
Building REAL250005071736
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071736'
/scratch/stefan/7916153/working/building/REAL250005071736 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071736

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071736/0 /scratch/stefan/7916153/working/building/REAL250005071736 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 873)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/873
`/scratch/stefan/7916153/working/3D/873' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)N2CCCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1)

`REAL250005071736.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071736.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071736/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071736 none CC1(C(=O)N2CCCN(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', '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, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 5, 5] 31
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 17, 18, 24, 25, 26, 27, 28, 29, 31] set([0, 1, 3, 36, 37, 35, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 38, 30])
total number of confs: 39
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071736 none CC1(C(=O)N2CCCN(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', '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, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 19, 19, 31, 31, 31, 31, 31, 5, 5, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 31, 5, 5, 5, 5, 1, 1, 1, 1] 31
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: 74
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071736 none CC1(C(=O)N2CCCN(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', '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, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 15, 31, 15, 15, 15, 15, 10, 1, 10, 1, 1, 1, 1, 1, 1, 15, 15, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 1, 15, 15, 15, 15, 31, 31, 31, 31] 31
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: 81
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071736 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071736
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071736/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071736
Building REAL250005071737
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071737'
/scratch/stefan/7916153/working/building/REAL250005071737 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071737

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071737/0 /scratch/stefan/7916153/working/building/REAL250005071737 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 874)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/874
`/scratch/stefan/7916153/working/3D/874' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071737.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071737.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071737/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071737 none C[C@@H]1C[C@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 19, 19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 30, 1, 1, 1, 1] 72
rigid atoms, others: [32, 33, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 21, 22, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 34, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27])
total number of confs: 92
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071737 none C[C@@H]1C[C@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 7, 7, 19, 19, 19, 19, 19, 51, 51, 72, 72, 72, 72, 72, 19, 19, 2, 2, 2, 1, 1, 19, 19, 19, 19, 19, 19, 72, 19, 19, 19, 19] 72
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: 171
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071737 none C[C@@H]1C[C@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 60, 72, 30, 60, 30, 30, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 30, 72, 72, 72, 72, 72, 30, 30, 30, 30, 30, 30, 1, 30, 30, 30, 30] 72
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: 188
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071737 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071737
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071737/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071737
Building REAL250005071738
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071738'
/scratch/stefan/7916153/working/building/REAL250005071738 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071738

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071738/0 /scratch/stefan/7916153/working/building/REAL250005071738 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 875)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/875
`/scratch/stefan/7916153/working/3D/875' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071738.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071738.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071738/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071738 none CCC(F)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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, 53, 75, 25, 53, 25, 25, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 75, 75, 75, 75, 75, 75, 25, 25, 25, 25, 25, 25, 1, 25, 25, 25, 25] 75
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: 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071738 none CCC(F)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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: [23, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 23, 23, 23, 23, 23, 13, 1, 1, 1, 1, 1, 1, 25, 1, 1, 1, 1] 75
rigid atoms, others: [32, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 33, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26])
total number of confs: 144
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071738 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071738
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071738/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071738
Building REAL250005071739
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071739'
/scratch/stefan/7916153/working/building/REAL250005071739 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071739

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071739/0 /scratch/stefan/7916153/working/building/REAL250005071739 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 876)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/876
`/scratch/stefan/7916153/working/3D/876' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCF)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071739.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071739.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071739/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071739 none O=C(CCCF)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 8, 5, 5, 5, 8, 1, 11, 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
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [70, 29, 70, 132, 155, 158, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 132, 132, 158, 158, 158, 158, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 158
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: 643
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071739 none O=C(CCCF)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 8, 5, 5, 5, 8, 1, 11, 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
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 20, 32, 55, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 20, 20, 33, 33, 55, 54, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 158
rigid atoms, others: [32, 1, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30, 31] set([0, 33, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26])
total number of confs: 301
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071739 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071739
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071739/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071739
Building REAL250005071740
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071740'
/scratch/stefan/7916153/working/building/REAL250005071740 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071740

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071740/0 /scratch/stefan/7916153/working/building/REAL250005071740 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 877)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/877
`/scratch/stefan/7916153/working/3D/877' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1C[C@@H]1C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071740.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071740.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071740/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071740 none C[C@H]1C[C@@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 7, 20, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 28, 1, 1, 1, 1] 78
rigid atoms, others: [32, 33, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 21, 22, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 34, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27])
total number of confs: 94
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071740 none C[C@H]1C[C@@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 20, 53, 53, 78, 78, 78, 78, 78, 20, 20, 2, 2, 2, 1, 1, 20, 20, 20, 20, 20, 20, 78, 20, 20, 20, 20] 78
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: 180
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071740 none C[C@H]1C[C@@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 56, 78, 28, 56, 28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 78, 78, 78, 78, 78, 28, 28, 28, 28, 28, 28, 1, 28, 28, 28, 28] 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, 37, 38])
total number of confs: 224
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071740 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071740
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071740/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071740
Building REAL250005071741
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071741'
/scratch/stefan/7916153/working/building/REAL250005071741 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071741

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071741/0 /scratch/stefan/7916153/working/building/REAL250005071741 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 878)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/878
`/scratch/stefan/7916153/working/3D/878' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071741.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071741.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071741/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071741 none NC(=O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 40, 52, 23, 40, 23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 52, 52, 23, 23, 23, 23, 23, 23, 1, 23, 23, 23, 23] 52
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: 146
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071741 none NC(=O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 14, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 15, 15, 1, 1, 1, 1, 1, 1, 23, 1, 1, 1, 1] 52
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 28])
total number of confs: 74
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071741 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071741
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071741/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071741
Building REAL250005071742
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071742'
/scratch/stefan/7916153/working/building/REAL250005071742 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071742

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071742/0 /scratch/stefan/7916153/working/building/REAL250005071742 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 879)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/879
`/scratch/stefan/7916153/working/3D/879' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071742.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071742.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071742/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071742 none CC(C)(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 11, 11, 11, 11] 11
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: 22
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071742 none CC(C)(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1] 11
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 19, 20, 39, 38, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 26
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071742 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071742
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071742/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071742
Building REAL250005071743
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071743'
/scratch/stefan/7916153/working/building/REAL250005071743 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071743

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071743/0 /scratch/stefan/7916153/working/building/REAL250005071743 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 880)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/880
`/scratch/stefan/7916153/working/3D/880' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071743.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071743.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071743/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071743 none C=CCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 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
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [94, 94, 61, 27, 61, 27, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 94, 94, 94, 94, 94, 27, 27, 27, 27, 27, 27, 1, 27, 27, 27, 27] 94
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: 320
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071743 none C=CCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 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
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [41, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 41, 41, 41, 20, 20, 1, 1, 1, 1, 1, 1, 27, 1, 1, 1, 1] 94
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 29, 30, 35] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31])
total number of confs: 176
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071743 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071743
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071743/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071743
Building REAL250005071744
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071744'
/scratch/stefan/7916153/working/building/REAL250005071744 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071744

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071744/0 /scratch/stefan/7916153/working/building/REAL250005071744 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 881)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/881
`/scratch/stefan/7916153/working/3D/881' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071744.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071744.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071744/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071744 none C[NH+](C)CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7] 7
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: 15
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071744 none C[NH+](C)CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 1, 1, 1, 1] 7
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 12, 40, 20, 21, 39, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 34
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071744 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071744/1 /scratch/stefan/7916153/working/building/REAL250005071744 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 882)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/882
`/scratch/stefan/7916153/working/3D/882' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071744.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071744.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071744/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071744 none CN(C)CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 62, 29, 62, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 103, 103, 103, 103, 103, 103, 99, 99, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 103
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: 350
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071744 none CN(C)CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 23, 36, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 36, 36, 36, 36, 36, 36, 23, 23, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 103
rigid atoms, others: [32, 33, 34, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 39, 36, 38, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 35, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 170
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071744 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071744
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071744/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071744/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071744
Building REAL250005071745
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071745'
/scratch/stefan/7916153/working/building/REAL250005071745 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071745

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071745/0 /scratch/stefan/7916153/working/building/REAL250005071745 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 883)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/883
`/scratch/stefan/7916153/working/3D/883' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(O)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071745.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071745.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071745/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071745 none C=CC(O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 50, 62, 24, 50, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 62, 62, 62, 62, 186, 24, 24, 24, 24, 24, 24, 1, 24, 24, 24, 24] 186
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: 368
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071745 none C=CC(O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [33, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 33, 33, 33, 16, 48, 1, 1, 1, 1, 1, 1, 24, 1, 1, 1, 1] 186
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25])
total number of confs: 191
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071745 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071745
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071745/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071745
Building REAL250005071746
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071746'
/scratch/stefan/7916153/working/building/REAL250005071746 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071746

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071746/0 /scratch/stefan/7916153/working/building/REAL250005071746 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 884)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/884
`/scratch/stefan/7916153/working/3D/884' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCCN(C(=O)C2COC2)CC1)

`REAL250005071746.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071746.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071746/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071746 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 1, 1, 28, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 1, 1, 1, 1] 57
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 28, 29, 30, 31])
total number of confs: 78
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071746 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 1, 10, 28, 28, 28, 28, 28, 48, 48, 57, 57, 57, 28, 28, 1, 28, 28, 28, 28, 28, 28, 57, 57, 57, 57, 57, 28, 28, 28, 28] 57
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: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071746 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [45, 14, 45, 57, 57, 57, 57, 57, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 1, 14, 14, 57, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 14, 14, 14, 14] 57
rigid atoms, others: [32, 13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36])
total number of confs: 136
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071746 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071746
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071746/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071746
Building REAL250005071747
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071747'
/scratch/stefan/7916153/working/building/REAL250005071747 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071747

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071747/0 /scratch/stefan/7916153/working/building/REAL250005071747 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 885)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/885
`/scratch/stefan/7916153/working/3D/885' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CO[C@H](C)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071747.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071747.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071747/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071747 none CO[C@H](C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 37, 28, 37, 37, 18, 28, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 18, 45, 45, 45, 37, 37, 37, 18, 18, 18, 18, 18, 18, 1, 18, 18, 18, 18] 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, 37, 38])
total number of confs: 135
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071747 none CO[C@H](C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 11, 7, 11, 11, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 1, 1, 15, 15, 15, 11, 11, 11, 1, 1, 1, 1, 1, 1, 18, 1, 1, 1, 1] 45
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 34, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27])
total number of confs: 74
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071747 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071747
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071747/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071747
Building REAL250005071748
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071748'
/scratch/stefan/7916153/working/building/REAL250005071748 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071748

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071748/0 /scratch/stefan/7916153/working/building/REAL250005071748 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 886)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/886
`/scratch/stefan/7916153/working/3D/886' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071748.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071748.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071748/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071748 none CCC=CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [140, 121, 121, 78, 31, 78, 31, 31, 31, 31, 10, 1, 10, 1, 1, 1, 1, 1, 1, 31, 31, 140, 140, 140, 140, 140, 121, 121, 31, 31, 31, 31, 31, 31, 1, 31, 31, 31, 31] 140
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: 451
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071748 none CCC=CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [51, 24, 24, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 51, 51, 51, 51, 51, 24, 24, 1, 1, 1, 1, 1, 1, 31, 1, 1, 1, 1] 140
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 246
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071748 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071748
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071748/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071748
Building REAL250005071749
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071749'
/scratch/stefan/7916153/working/building/REAL250005071749 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL250005071749 as failed and skipping
/scratch/stefan/7916153/working /scratch/stefan/7916153
`/scratch/stefan/7916153/working/building/REAL250005071749' -> `/scratch/stefan/7916153/failed/REAL250005071749'
Building REAL250005071750
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071750'
/scratch/stefan/7916153/working/building/REAL250005071750 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071750

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071750/0 /scratch/stefan/7916153/working/building/REAL250005071750 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 887)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/887
`/scratch/stefan/7916153/working/3D/887' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071750.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071750.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071750/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071750 none O=C(CO)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 12, 8, 5, 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]
dock color type numbers: [6, 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]
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, 29, 52, 59, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 59, 59, 177, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 177
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: 346
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071750 none O=C(CO)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 12, 8, 5, 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]
dock color type numbers: [6, 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]
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, 1, 6, 14, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 14, 14, 42, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 177
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 17, 18, 22, 23, 24, 25, 26, 27, 29, 30, 31] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 28])
total number of confs: 130
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071750 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071750
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071750/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071750
Building REAL250005071751
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071751'
/scratch/stefan/7916153/working/building/REAL250005071751 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071751

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071751/0 /scratch/stefan/7916153/working/building/REAL250005071751 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 888)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/888
`/scratch/stefan/7916153/working/3D/888' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071751.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071751.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071751/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071751 none CC(O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 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]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [54, 51, 54, 26, 51, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 54, 54, 54, 54, 162, 26, 26, 26, 26, 26, 26, 1, 26, 26, 26, 26] 162
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: 301
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071751 none CC(O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 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]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 18, 18, 18, 18, 54, 1, 1, 1, 1, 1, 1, 26, 1, 1, 1, 1] 162
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 29, 30, 35] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31])
total number of confs: 159
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071751 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071751
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071751/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071751
Building REAL250005071752
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071752'
/scratch/stefan/7916153/working/building/REAL250005071752 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071752

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071752/0 /scratch/stefan/7916153/working/building/REAL250005071752 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 889)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/889
`/scratch/stefan/7916153/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)N1CCCN(C(=O)C2CC2F)CC1)

`REAL250005071752.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071752.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071752/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071752 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', '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', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 1, 1, 28, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 1, 1, 1, 1] 63
rigid atoms, others: [32, 1, 34, 35, 33, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 28, 29, 30, 31])
total number of confs: 87
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071752 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', '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', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 1, 10, 28, 28, 28, 28, 28, 45, 45, 63, 63, 63, 28, 28, 1, 28, 28, 28, 28, 28, 28, 63, 63, 63, 63, 28, 28, 28, 28] 63
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: 179
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071752 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', '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', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [44, 18, 44, 63, 63, 63, 63, 63, 18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 18, 18, 63, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 18, 18, 18, 18] 63
rigid atoms, others: [13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 141
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071752 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071752
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071752/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071752
Building REAL250005071753
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071753'
/scratch/stefan/7916153/working/building/REAL250005071753 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071753

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071753/0 /scratch/stefan/7916153/working/building/REAL250005071753 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 890)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/890
`/scratch/stefan/7916153/working/3D/890' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071753.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071753.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071753/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071753 none O=C(CCF)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 15, 8, 5, 5, 5, 8, 1, 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
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [46, 23, 46, 78, 78, 23, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 78, 78, 78, 78, 23, 23, 23, 23, 23, 23, 1, 23, 23, 23, 23] 78
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: 275
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071753 none O=C(CCF)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 15, 8, 5, 5, 5, 8, 1, 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
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 13, 27, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 13, 13, 27, 27, 1, 1, 1, 1, 1, 1, 23, 1, 1, 1, 1] 78
rigid atoms, others: [32, 1, 34, 33, 5, 6, 7, 8, 9, 10, 18, 19, 24, 25, 26, 27, 28, 29, 31] set([0, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 30])
total number of confs: 149
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071753 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071753
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071753/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071753
Building REAL250005071754
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071754'
/scratch/stefan/7916153/working/building/REAL250005071754 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071754

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071754/0 /scratch/stefan/7916153/working/building/REAL250005071754 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 891)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/891
`/scratch/stefan/7916153/working/3D/891' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCF)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071754.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071754.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071754/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071754 none O=C(C=CCF)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 1, 5, 15, 8, 5, 5, 5, 8, 1, 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, 7, 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
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [66, 29, 66, 96, 96, 100, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 96, 96, 100, 100, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 100
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: 284
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071754 none O=C(C=CCF)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 1, 5, 15, 8, 5, 5, 5, 8, 1, 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, 7, 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
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 27, 27, 60, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 27, 27, 60, 60, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 100
rigid atoms, others: [32, 1, 34, 35, 33, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 31])
total number of confs: 253
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071754 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071754
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071754/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071754
Building REAL250005071755
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071755'
/scratch/stefan/7916153/working/building/REAL250005071755 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071755

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071755/0 /scratch/stefan/7916153/working/building/REAL250005071755 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 892)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/892
`/scratch/stefan/7916153/working/3D/892' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071755.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071755.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071755/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071755 none C#CCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [91, 91, 88, 59, 26, 59, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 91, 91, 91, 88, 88, 26, 26, 26, 26, 26, 26, 1, 26, 26, 26, 26] 91
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: 300
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071755 none C#CCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 30, 30, 30, 18, 18, 1, 1, 1, 1, 1, 1, 26, 1, 1, 1, 1] 91
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25])
total number of confs: 169
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071755 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071755
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071755/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071755
Building REAL250005071756
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071756'
/scratch/stefan/7916153/working/building/REAL250005071756 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071756

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071756/0 /scratch/stefan/7916153/working/building/REAL250005071756 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 893)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/893
`/scratch/stefan/7916153/working/3D/893' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCCN(C(=O)C2CCO2)CC1)

`REAL250005071756.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071756.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071756/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071756 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 7, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 1, 1, 18, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 1] 41
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 28, 29, 30, 31])
total number of confs: 66
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071756 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 18, 34, 34, 41, 41, 41, 18, 18, 1, 18, 18, 18, 18, 18, 18, 41, 41, 41, 41, 41, 18, 18, 18, 18] 41
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: 112
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071756 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [31, 13, 31, 41, 41, 41, 41, 41, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 1, 13, 13, 41, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 13, 13, 13, 13] 41
rigid atoms, others: [32, 13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36])
total number of confs: 94
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071756 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071756
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071756/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071756
Building REAL250005071757
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071757'
/scratch/stefan/7916153/working/building/REAL250005071757 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071757

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071757/0 /scratch/stefan/7916153/working/building/REAL250005071757 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 894)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/894
`/scratch/stefan/7916153/working/3D/894' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(O)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071757.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071757.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071757/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071757 none CC(C)(O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 28, 39, 39, 17, 28, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 39, 39, 39, 39, 39, 39, 117, 17, 17, 17, 17, 17, 17, 1, 17, 17, 17, 17] 117
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: 259
number of broken/clashed sets: 53
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071757 none CC(C)(O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 4, 6, 6, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 1, 1, 6, 6, 6, 6, 6, 6, 18, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1] 117
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 69
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071757 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071757
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071757/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071757
Building REAL250005071758
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071758'
/scratch/stefan/7916153/working/building/REAL250005071758 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071758

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071758/0 /scratch/stefan/7916153/working/building/REAL250005071758 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 895)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/895
`/scratch/stefan/7916153/working/3D/895' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071758.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071758.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071758/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071758 none CC1=CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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: [20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 27, 1, 1, 1, 1] 72
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25])
total number of confs: 91
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071758 none CC1=CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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, 20, 20, 20, 20, 20, 54, 54, 72, 72, 72, 72, 72, 20, 20, 2, 2, 2, 1, 1, 20, 20, 20, 20, 20, 20, 72, 20, 20, 20, 20] 72
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: 172
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071758 none CC1=CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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, 56, 27, 56, 27, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 72, 72, 72, 72, 72, 27, 27, 27, 27, 27, 27, 1, 27, 27, 27, 27] 72
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: 198
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071758 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071758
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071758/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071758
Building REAL250005071759
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071759'
/scratch/stefan/7916153/working/building/REAL250005071759 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071759

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071759/0 /scratch/stefan/7916153/working/building/REAL250005071759 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 896)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/896
`/scratch/stefan/7916153/working/3D/896' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071759.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071759.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071759/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071759 none C[C@@H](O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 7, 12, 1, 11, 8, 5, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 31, 33, 33, 19, 31, 19, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 33, 33, 33, 99, 19, 19, 19, 19, 19, 19, 1, 19, 19, 19, 19] 99
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: 185
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071759 none C[C@@H](O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 7, 12, 1, 11, 8, 5, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 6, 10, 10, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 10, 10, 10, 30, 1, 1, 1, 1, 1, 1, 19, 1, 1, 1, 1] 99
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 31])
total number of confs: 95
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071759 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071759
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071759/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071759
Building REAL250005071760
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071760'
/scratch/stefan/7916153/working/building/REAL250005071760 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071760

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071760/0 /scratch/stefan/7916153/working/building/REAL250005071760 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 897)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/897
`/scratch/stefan/7916153/working/3D/897' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCO)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071760.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071760.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071760/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071760 none O=C(C=CCO)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 12, 8, 5, 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]
dock color type numbers: [6, 7, 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]
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: [72, 31, 72, 131, 131, 136, 31, 31, 31, 31, 10, 1, 10, 1, 1, 1, 1, 1, 1, 31, 31, 131, 131, 136, 136, 408, 31, 31, 31, 31, 31, 31, 1, 31, 31, 31, 31] 408
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: 798
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071760 none O=C(C=CCO)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 12, 8, 5, 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]
dock color type numbers: [6, 7, 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]
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: [6, 1, 6, 26, 26, 70, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 26, 26, 70, 70, 210, 1, 1, 1, 1, 1, 1, 31, 1, 1, 1, 1] 408
rigid atoms, others: [1, 34, 35, 36, 33, 6, 7, 8, 9, 10, 11, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25])
total number of confs: 499
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071760 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071760
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071760/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071760
Building REAL250005071761
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071761'
/scratch/stefan/7916153/working/building/REAL250005071761 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071761

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071761/0 /scratch/stefan/7916153/working/building/REAL250005071761 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 898)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/898
`/scratch/stefan/7916153/working/3D/898' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CCC1)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071761.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071761.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071761/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071761 none O=C(C1=CCC1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 8, 5, 5, 5, 8, 1, 11, 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
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 12, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 22, 1, 1, 1, 1] 39
rigid atoms, others: [1, 34, 35, 36, 33, 6, 7, 8, 9, 10, 11, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071761 none O=C(C1=CCC1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 8, 5, 5, 5, 8, 1, 11, 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
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [8, 1, 1, 1, 1, 1, 8, 12, 12, 12, 12, 12, 30, 30, 39, 39, 39, 39, 39, 12, 12, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 39, 12, 12, 12, 12] 39
rigid atoms, others: [1, 2, 3, 4, 5, 21, 22, 23, 24, 25] set([0, 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: 96
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071761 none O=C(C1=CCC1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 8, 5, 5, 5, 8, 1, 11, 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
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [39, 22, 39, 39, 39, 39, 22, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 39, 39, 39, 39, 39, 22, 22, 22, 22, 22, 22, 1, 22, 22, 22, 22] 39
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: 90
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071761 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071761
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071761/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071761
Building REAL250005071762
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071762'
/scratch/stefan/7916153/working/building/REAL250005071762 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071762

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071762/0 /scratch/stefan/7916153/working/building/REAL250005071762 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 899)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/899
`/scratch/stefan/7916153/working/3D/899' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071762.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071762.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071762/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071762 none CON=CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 43, 21, 43, 21, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 70, 70, 70, 70, 21, 21, 21, 21, 21, 21, 1, 21, 21, 21, 21] 70
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: 198
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071762 none CON=CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 27, 27, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 38, 38, 38, 27, 1, 1, 1, 1, 1, 1, 21, 1, 1, 1, 1] 70
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 31])
total number of confs: 123
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071762 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071762
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071762/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071762
Building REAL250005071763
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071763'
/scratch/stefan/7916153/working/building/REAL250005071763 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071763

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071763/0 /scratch/stefan/7916153/working/building/REAL250005071763 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 900)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/900
`/scratch/stefan/7916153/working/3D/900' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCCN(C(=O)C2(F)CC2)CC1)

`REAL250005071763.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071763.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071763/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071763 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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: [7, 1, 7, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 1, 1, 22, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 1, 1, 1, 1] 52
rigid atoms, others: [32, 1, 34, 35, 33, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 28, 29, 30, 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071763 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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: [10, 1, 1, 1, 1, 1, 1, 1, 10, 22, 22, 22, 22, 22, 33, 33, 52, 52, 52, 22, 22, 1, 22, 22, 22, 22, 22, 22, 52, 52, 52, 52, 22, 22, 22, 22] 52
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: 157
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071763 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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: [37, 15, 37, 52, 52, 52, 52, 52, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 15, 15, 52, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 15, 15, 15, 15] 52
rigid atoms, others: [13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 112
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071763 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071763
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071763/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071763
Building REAL250005071764
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071764'
/scratch/stefan/7916153/working/building/REAL250005071764 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071764

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071764/0 /scratch/stefan/7916153/working/building/REAL250005071764 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 901)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/901
`/scratch/stefan/7916153/working/3D/901' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(F)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071764.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071764.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071764/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071764 none CC=C(F)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 15, 1, 11, 8, 5, 5, 5, 8, 1, 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, 7, 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
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [96, 96, 67, 96, 26, 67, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 96, 96, 96, 96, 26, 26, 26, 26, 26, 26, 1, 26, 26, 26, 26] 96
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: 277
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071764 none CC=C(F)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 15, 1, 11, 8, 5, 5, 5, 8, 1, 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, 7, 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
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 7, 29, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 26, 1, 1, 1, 1] 96
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 31])
total number of confs: 110
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071764 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071764
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071764/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071764
Building REAL250005071765
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071765'
/scratch/stefan/7916153/working/building/REAL250005071765 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071765

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071765/0 /scratch/stefan/7916153/working/building/REAL250005071765 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 902)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/902
`/scratch/stefan/7916153/working/3D/902' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CO)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071765.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071765.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071765/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071765 none CC(CO)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 47, 52, 52, 24, 47, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 52, 52, 52, 52, 52, 52, 156, 24, 24, 24, 24, 24, 24, 1, 24, 24, 24, 24] 156
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: 302
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071765 none CC(CO)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 6, 12, 24, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 12, 12, 12, 12, 24, 24, 72, 1, 1, 1, 1, 1, 1, 24, 1, 1, 1, 1] 156
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 209
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071765 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071765
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071765/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071765
Building REAL250005071766
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071766'
/scratch/stefan/7916153/working/building/REAL250005071766 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071766

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071766/0 /scratch/stefan/7916153/working/building/REAL250005071766 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 903)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/903
`/scratch/stefan/7916153/working/3D/903' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071766.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071766.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071766/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071766 none C[C@H](O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 7, 12, 1, 11, 8, 5, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 44, 44, 23, 44, 23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 44, 44, 44, 132, 23, 23, 23, 23, 23, 23, 1, 23, 23, 23, 23] 132
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: 232
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071766 none C[C@H](O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 7, 12, 1, 11, 8, 5, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 7, 11, 11, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 11, 11, 11, 33, 1, 1, 1, 1, 1, 1, 23, 1, 1, 1, 1] 132
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 31])
total number of confs: 105
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071766 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071766
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071766/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071766
Building REAL250005071767
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071767'
/scratch/stefan/7916153/working/building/REAL250005071767 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071767

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071767/0 /scratch/stefan/7916153/working/building/REAL250005071767 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 904)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/904
`/scratch/stefan/7916153/working/3D/904' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071767.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071767.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071767/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071767 none C=C1CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 19, 1, 1, 1, 1] 62
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25])
total number of confs: 83
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071767 none C=C1CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 20, 50, 50, 62, 62, 62, 62, 62, 20, 20, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 62, 20, 20, 20, 20] 62
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: 144
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071767 none C=C1CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 42, 19, 42, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 62, 62, 62, 62, 62, 19, 19, 19, 19, 19, 19, 1, 19, 19, 19, 19] 62
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: 184
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071767 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071767
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071767/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071767
Building REAL250005071768
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071768'
/scratch/stefan/7916153/working/building/REAL250005071768 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071768

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071768/0 /scratch/stefan/7916153/working/building/REAL250005071768 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 905)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/905
`/scratch/stefan/7916153/working/3D/905' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CF)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071768.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071768.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071768/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071768 none CC(CF)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [57, 50, 57, 63, 26, 50, 26, 26, 26, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 26, 57, 57, 57, 57, 63, 63, 26, 26, 26, 26, 26, 26, 1, 26, 26, 26, 26] 63
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: 190
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071768 none CC(CF)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [12, 6, 12, 26, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 12, 12, 12, 12, 26, 26, 1, 1, 1, 1, 1, 1, 26, 1, 1, 1, 1] 63
rigid atoms, others: [32, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 33, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26])
total number of confs: 139
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071768 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071768
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071768/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071768
Building REAL250005071769
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071769'
/scratch/stefan/7916153/working/building/REAL250005071769 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071769

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071769/0 /scratch/stefan/7916153/working/building/REAL250005071769 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 906)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/906
`/scratch/stefan/7916153/working/3D/906' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071769.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071769.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071769/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071769 none C=C(C)CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 108, 64, 29, 64, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 108, 108, 108, 108, 108, 108, 108, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 108
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: 361
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071769 none C=C(C)CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [36, 24, 36, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 36, 36, 36, 36, 36, 24, 24, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 108
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 166
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071769 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071769
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071769/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071769
Building REAL250005071770
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071770'
/scratch/stefan/7916153/working/building/REAL250005071770 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071770

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071770/0 /scratch/stefan/7916153/working/building/REAL250005071770 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 907)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/907
`/scratch/stefan/7916153/working/3D/907' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071770.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071770.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071770/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071770 none CC=CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 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
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 53, 29, 53, 29, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 62, 62, 62, 62, 62, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 62
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: 154
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071770 none CC=CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 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
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 62
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 29, 30, 35] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31])
total number of confs: 85
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071770 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071770
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071770/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071770
Building REAL250005071771
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071771'
/scratch/stefan/7916153/working/building/REAL250005071771 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071771

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071771/0 /scratch/stefan/7916153/working/building/REAL250005071771 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 908)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/908
`/scratch/stefan/7916153/working/3D/908' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071771.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071771.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071771/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071771 none C[C@@H]1C[C@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 19, 19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 30, 1, 1, 1, 1] 72
rigid atoms, others: [32, 33, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 21, 22, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 34, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27])
total number of confs: 92
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071771 none C[C@@H]1C[C@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 7, 7, 19, 19, 19, 19, 19, 51, 51, 72, 72, 72, 72, 72, 19, 19, 2, 2, 2, 1, 1, 19, 19, 19, 19, 19, 19, 72, 19, 19, 19, 19] 72
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: 171
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071771 none C[C@@H]1C[C@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 60, 72, 30, 60, 30, 30, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 30, 72, 72, 72, 72, 72, 30, 30, 30, 30, 30, 30, 1, 30, 30, 30, 30] 72
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: 188
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071771 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071771
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071771/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071771
Building REAL250005071772
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071772'
/scratch/stefan/7916153/working/building/REAL250005071772 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071772

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071772/0 /scratch/stefan/7916153/working/building/REAL250005071772 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 909)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/909
`/scratch/stefan/7916153/working/3D/909' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCCN(C(=O)C2(O)CC2)CC1)

`REAL250005071772.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071772.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071772/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071772 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 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
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 1, 1, 20, 1, 1, 1, 1, 1, 1, 39, 13, 13, 13, 13, 1, 1, 1, 1] 144
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 28, 29, 30, 31])
total number of confs: 106
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071772 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 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
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 33, 33, 48, 48, 48, 20, 20, 1, 20, 20, 20, 20, 20, 20, 144, 48, 48, 48, 48, 20, 20, 20, 20] 144
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: 287
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071772 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 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
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [37, 13, 37, 48, 48, 48, 48, 48, 13, 13, 13, 13, 5, 1, 5, 1, 1, 1, 1, 13, 13, 48, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 13, 13, 13] 144
rigid atoms, others: [32, 13, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 115
number of broken/clashed sets: 34
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071772 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071772
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071772/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071772
Building REAL250005071773
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071773'
/scratch/stefan/7916153/working/building/REAL250005071773 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071773

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071773/0 /scratch/stefan/7916153/working/building/REAL250005071773 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 910)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/910
`/scratch/stefan/7916153/working/3D/910' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC1)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071773.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071773.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071773/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071773 none O=C(CC1CC1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 8, 5, 5, 5, 8, 1, 11, 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
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 23, 33, 33, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 23, 23, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 124
rigid atoms, others: [32, 1, 35, 36, 33, 6, 7, 8, 9, 10, 11, 37, 19, 20, 38, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 162
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071773 none O=C(CC1CC1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 8, 5, 5, 5, 8, 1, 11, 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
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [14, 3, 1, 1, 1, 1, 14, 33, 33, 33, 33, 33, 87, 87, 124, 124, 124, 124, 124, 33, 33, 3, 3, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 124, 33, 33, 33, 33] 124
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: 285
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071773 none O=C(CC1CC1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 8, 5, 5, 5, 8, 1, 11, 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
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [79, 29, 79, 99, 124, 124, 29, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 99, 99, 124, 124, 124, 124, 124, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 124
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: 410
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071773 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071773
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071773/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071773
Building REAL250005071774
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071774'
/scratch/stefan/7916153/working/building/REAL250005071774 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071774

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071774/0 /scratch/stefan/7916153/working/building/REAL250005071774 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 911)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/911
`/scratch/stefan/7916153/working/3D/911' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(F)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071774.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071774.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071774/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071774 none CC(C)(F)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 39, 45, 45, 22, 39, 22, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 45, 45, 45, 45, 45, 45, 22, 22, 22, 22, 22, 22, 1, 22, 22, 22, 22] 45
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: 130
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071774 none CC(C)(F)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [9, 6, 9, 9, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 22, 1, 1, 1, 1] 45
rigid atoms, others: [32, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 33, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26])
total number of confs: 66
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071774 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071774
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071774/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071774
Building REAL250005071775
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071775'
/scratch/stefan/7916153/working/building/REAL250005071775 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071775

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071775/0 /scratch/stefan/7916153/working/building/REAL250005071775 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 912)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/912
`/scratch/stefan/7916153/working/3D/912' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071775.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071775.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071775/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071775 none COCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 61, 29, 61, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 97, 97, 97, 96, 96, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 97
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: 334
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071775 none COCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 34, 34, 34, 16, 16, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 97
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 29, 30, 35] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31])
total number of confs: 132
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071775 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071775
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071775/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071775
Building REAL250005071776
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071776'
/scratch/stefan/7916153/working/building/REAL250005071776 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071776

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071776/0 /scratch/stefan/7916153/working/building/REAL250005071776 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 913)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/913
`/scratch/stefan/7916153/working/3D/913' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071776.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071776.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071776/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071776 none CCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 50, 25, 50, 25, 25, 25, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 85, 85, 85, 85, 85, 85, 85, 25, 25, 25, 25, 25, 25, 1, 25, 25, 25, 25] 85
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: 291
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071776 none CCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [24, 18, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 26, 26, 26, 25, 25, 18, 18, 1, 1, 1, 1, 1, 1, 25, 1, 1, 1, 1] 85
rigid atoms, others: [32, 35, 34, 3, 36, 5, 6, 7, 8, 9, 10, 37, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 33, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 157
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071776 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071776
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071776/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071776
Building REAL250005071777
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071777'
/scratch/stefan/7916153/working/building/REAL250005071777 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071777

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071777/0 /scratch/stefan/7916153/working/building/REAL250005071777 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 914)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/914
`/scratch/stefan/7916153/working/3D/914' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071777.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071777.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071777/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071777 none CC(C)CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 38, 18, 38, 18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 52, 52, 52, 52, 52, 52, 52, 52, 52, 18, 18, 18, 18, 18, 18, 1, 18, 18, 18, 18] 52
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: 172
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071777 none CC(C)CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [13, 11, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 1, 1, 13, 13, 13, 13, 13, 13, 13, 11, 11, 1, 1, 1, 1, 1, 1, 18, 1, 1, 1, 1] 52
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 19, 20, 39, 38, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 77
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071777 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071777
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071777/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071777
Building REAL250005071778
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071778'
/scratch/stefan/7916153/working/building/REAL250005071778 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071778

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071778/0 /scratch/stefan/7916153/working/building/REAL250005071778 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 915)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/915
`/scratch/stefan/7916153/working/3D/915' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071778.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071778.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071778/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071778 none CC1CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 23, 1, 1, 1, 1] 67
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 93
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071778 none CC1CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 54, 54, 67, 67, 67, 67, 67, 22, 22, 2, 2, 2, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 67, 22, 22, 22, 22] 67
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: 157
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071778 none CC1CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 51, 23, 51, 23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 67, 67, 67, 67, 67, 67, 67, 23, 23, 23, 23, 23, 23, 1, 23, 23, 23, 23] 67
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: 191
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071778 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071778
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071778/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071778
Building REAL250005071779
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071779'
/scratch/stefan/7916153/working/building/REAL250005071779 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071779

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071779/0 /scratch/stefan/7916153/working/building/REAL250005071779 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 916)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/916
`/scratch/stefan/7916153/working/3D/916' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071779.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071779.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071779/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071779 none CCOCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 167, 136, 73, 28, 73, 28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 168, 168, 168, 168, 168, 136, 136, 28, 28, 28, 28, 28, 28, 1, 28, 28, 28, 28] 168
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: 545
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071779 none CCOCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [64, 55, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 65, 65, 65, 64, 64, 22, 22, 1, 1, 1, 1, 1, 1, 28, 1, 1, 1, 1] 168
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 226
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071779 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071779
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071779/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071779
Building REAL250005071780
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071780'
/scratch/stefan/7916153/working/building/REAL250005071780 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071780

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071780/0 /scratch/stefan/7916153/working/building/REAL250005071780 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 917)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/917
`/scratch/stefan/7916153/working/3D/917' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071780.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071780.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071780/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071780 none CC(C)=CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 48, 25, 48, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 67, 67, 67, 67, 67, 67, 67, 25, 25, 25, 25, 25, 25, 1, 25, 25, 25, 25] 67
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: 194
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071780 none CC(C)=CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 25, 1, 1, 1, 1] 67
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 89
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071780 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071780
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071780/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071780
Building REAL250005071781
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071781'
/scratch/stefan/7916153/working/building/REAL250005071781 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071781

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071781/0 /scratch/stefan/7916153/working/building/REAL250005071781 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 918)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/918
`/scratch/stefan/7916153/working/3D/918' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071781.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071781.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071781/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071781 none CSCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 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
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [137, 108, 73, 30, 73, 30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 137, 137, 137, 108, 108, 30, 30, 30, 30, 30, 30, 1, 30, 30, 30, 30] 137
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: 410
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071781 none CSCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 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
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [52, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 52, 52, 52, 22, 22, 1, 1, 1, 1, 1, 1, 30, 1, 1, 1, 1] 137
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 29, 30, 35] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31])
total number of confs: 167
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071781 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071781
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071781/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071781
Building REAL250005071782
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071782'
/scratch/stefan/7916153/working/building/REAL250005071782 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071782

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071782/0 /scratch/stefan/7916153/working/building/REAL250005071782 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 919)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/919
`/scratch/stefan/7916153/working/3D/919' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071782.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071782.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071782/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071782 none CCCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [99, 96, 87, 52, 24, 52, 24, 24, 24, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 99, 99, 99, 99, 99, 96, 96, 87, 87, 24, 24, 24, 24, 24, 24, 1, 24, 24, 24, 24] 99
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: 369
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071782 none CCCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 23, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 34, 34, 34, 33, 33, 24, 24, 15, 15, 1, 1, 1, 1, 1, 1, 24, 1, 1, 1, 1] 99
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 19, 20, 39, 38, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 198
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071782 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071782
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071782/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071782
Building REAL250005071783
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071783'
/scratch/stefan/7916153/working/building/REAL250005071783 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071783

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071783/0 /scratch/stefan/7916153/working/building/REAL250005071783 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 920)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/920
`/scratch/stefan/7916153/working/3D/920' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071783.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071783.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071783/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071783 none CC(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 20, 39, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 39, 39, 39, 39, 39, 39, 39, 20, 20, 20, 20, 20, 20, 1, 20, 20, 20, 20] 39
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: 96
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071783 none CC(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [9, 6, 9, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 20, 1, 1, 1, 1] 39
rigid atoms, others: [32, 35, 34, 3, 36, 5, 6, 7, 8, 9, 10, 37, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 33, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 64
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071783 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071783
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071783/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071783
Building REAL250005071784
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071784'
/scratch/stefan/7916153/working/building/REAL250005071784 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071784

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071784/0 /scratch/stefan/7916153/working/building/REAL250005071784 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 921)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/921
`/scratch/stefan/7916153/working/3D/921' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071784.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071784.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071784/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071784 none CCC(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 77, 64, 77, 26, 64, 26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 81, 81, 81, 81, 81, 77, 77, 77, 77, 26, 26, 26, 26, 26, 26, 1, 26, 26, 26, 26] 81
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: 251
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071784 none CCC(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 20, 20, 20, 20, 20, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 26, 1, 1, 1, 1] 81
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 19, 20, 39, 38, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 133
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071784 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071784
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071784/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071784
Building REAL250005071785
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071785'
/scratch/stefan/7916153/working/building/REAL250005071785 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071785

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071785/0 /scratch/stefan/7916153/working/building/REAL250005071785 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 922)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/922
`/scratch/stefan/7916153/working/3D/922' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071785.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071785.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071785/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071785 none COC(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 45, 36, 45, 20, 36, 20, 20, 20, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 47, 47, 47, 45, 45, 45, 45, 20, 20, 20, 20, 20, 20, 1, 20, 20, 20, 20] 47
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: 143
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071785 none COC(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 12, 5, 12, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 21, 21, 21, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 20, 1, 1, 1, 1] 47
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 92
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071785 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071785
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071785/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071785
Building REAL250005071786
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071786'
/scratch/stefan/7916153/working/building/REAL250005071786 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071786

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071786/0 /scratch/stefan/7916153/working/building/REAL250005071786 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 923)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/923
`/scratch/stefan/7916153/working/3D/923' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071786.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071786.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071786/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071786 none C=CCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [105, 105, 89, 49, 27, 49, 27, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 105, 105, 105, 105, 105, 89, 89, 27, 27, 27, 27, 27, 27, 1, 27, 27, 27, 27] 105
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: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071786 none C=CCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [44, 26, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 44, 44, 44, 26, 26, 15, 15, 1, 1, 1, 1, 1, 1, 27, 1, 1, 1, 1] 105
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 214
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071786 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071786
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071786/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071786
Building REAL250005071787
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071787'
/scratch/stefan/7916153/working/building/REAL250005071787 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071787

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071787/0 /scratch/stefan/7916153/working/building/REAL250005071787 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 924)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/924
`/scratch/stefan/7916153/working/3D/924' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C#N)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071787.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071787.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071787/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071787 none CC(C#N)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 8, 1, 11, 8, 5, 5, 5, 8, 1, 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, 7, 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
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [54, 46, 54, 54, 24, 46, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 54, 54, 54, 54, 24, 24, 24, 24, 24, 24, 1, 24, 24, 24, 24] 54
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: 160
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071787 none CC(C#N)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 8, 1, 11, 8, 5, 5, 5, 8, 1, 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, 7, 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
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [15, 7, 15, 15, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 24, 1, 1, 1, 1] 54
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 31])
total number of confs: 91
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071787 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071787
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071787/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071787
Building REAL250005071788
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071788'
/scratch/stefan/7916153/working/building/REAL250005071788 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071788

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071788/0 /scratch/stefan/7916153/working/building/REAL250005071788 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 925)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/925
`/scratch/stefan/7916153/working/3D/925' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(C)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071788.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071788.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071788/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071788 none CC=C(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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, 56, 36, 56, 21, 36, 21, 21, 21, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 21, 56, 56, 56, 56, 56, 56, 56, 21, 21, 21, 21, 21, 21, 1, 21, 21, 21, 21] 56
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: 174
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071788 none CC=C(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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: [14, 14, 7, 14, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 21, 1, 1, 1, 1] 56
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 74
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071788 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071788
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071788/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071788
Building REAL250005071789
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071789'
/scratch/stefan/7916153/working/building/REAL250005071789 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071789

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071789/0 /scratch/stefan/7916153/working/building/REAL250005071789 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 926)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/926
`/scratch/stefan/7916153/working/3D/926' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071789.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071789.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071789/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071789 none CCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 29, 18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 29, 29, 29, 29, 29, 18, 18, 18, 18, 18, 18, 1, 18, 18, 18, 18] 29
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: 72
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071789 none CCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 1, 1, 8, 8, 8, 7, 7, 1, 1, 1, 1, 1, 1, 18, 1, 1, 1, 1] 29
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 17, 18, 24, 25, 26, 27, 28, 29, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 30])
total number of confs: 60
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071789 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071789
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071789/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071789
Building REAL250005071790
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071790'
/scratch/stefan/7916153/working/building/REAL250005071790 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071790

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071790/0 /scratch/stefan/7916153/working/building/REAL250005071790 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 927)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/927
`/scratch/stefan/7916153/working/3D/927' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071790.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071790.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071790/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071790 none COCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 78, 50, 25, 50, 25, 25, 25, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 90, 90, 90, 90, 90, 78, 78, 25, 25, 25, 25, 25, 25, 1, 25, 25, 25, 25] 90
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: 320
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071790 none COCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [41, 23, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 41, 41, 41, 23, 23, 15, 15, 1, 1, 1, 1, 1, 1, 25, 1, 1, 1, 1] 90
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 158
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071790 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071790
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071790/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071790
Building REAL250005071791
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071791'
/scratch/stefan/7916153/working/building/REAL250005071791 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071791

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071791/0 /scratch/stefan/7916153/working/building/REAL250005071791 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 928)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/928
`/scratch/stefan/7916153/working/3D/928' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071791.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071791.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071791/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071791 none CC(=O)N1CCCN(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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 11, 8, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 19, 28, 19, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 28, 28, 28, 19, 19, 19, 19, 19, 19, 1, 19, 19, 19, 19] 28
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: 70
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071791 none CC(=O)N1CCCN(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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 11, 8, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 19, 1, 1, 1, 1] 28
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 16, 17, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 27])
total number of confs: 44
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071791 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071791
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071791/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071791
Building REAL250005071792
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071792'
/scratch/stefan/7916153/working/building/REAL250005071792 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071792

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071792/0 /scratch/stefan/7916153/working/building/REAL250005071792 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 929)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/929
`/scratch/stefan/7916153/working/3D/929' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCCN(C(=O)C2CC2)CC1)

`REAL250005071792.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071792.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071792/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071792 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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: [7, 1, 7, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 1, 1, 13, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 1, 1] 34
rigid atoms, others: [32, 1, 34, 35, 33, 8, 9, 10, 11, 12, 13, 18, 19, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 27, 28, 29, 30, 31])
total number of confs: 45
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071792 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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: [8, 1, 1, 1, 1, 1, 1, 1, 8, 13, 13, 13, 13, 13, 20, 20, 34, 34, 13, 13, 1, 13, 13, 13, 13, 13, 13, 34, 34, 34, 34, 34, 13, 13, 13, 13] 34
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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071792 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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: [24, 8, 24, 34, 34, 34, 34, 34, 8, 8, 8, 8, 5, 1, 5, 1, 1, 1, 8, 8, 34, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8] 34
rigid atoms, others: [13, 15, 16, 17, 27, 28, 29, 30, 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, 32, 33, 34, 35])
total number of confs: 79
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071792 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071792
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071792/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071792
Building REAL250005071793
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071793'
/scratch/stefan/7916153/working/building/REAL250005071793 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071793

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071793/0 /scratch/stefan/7916153/working/building/REAL250005071793 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 930)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/930
`/scratch/stefan/7916153/working/3D/930' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCCN(C(=O)C2CCC2)CC1)

`REAL250005071793.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071793.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071793/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071793 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 1, 1, 27, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1] 65
rigid atoms, others: [1, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 3, 4, 5, 6, 7, 34, 14, 15, 16, 17, 18, 21, 33, 28, 29, 30, 31])
total number of confs: 93
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071793 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 1, 10, 27, 27, 27, 27, 27, 54, 54, 65, 65, 65, 27, 27, 1, 27, 27, 27, 27, 27, 27, 65, 65, 65, 65, 65, 65, 65, 27, 27, 27, 27] 65
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: 174
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071793 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [53, 20, 53, 65, 65, 65, 65, 65, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 20, 20, 65, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20] 65
rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38])
total number of confs: 152
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071793 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071793
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071793/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071793
Building REAL250005071794
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071794'
/scratch/stefan/7916153/working/building/REAL250005071794 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071794

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071794/0 /scratch/stefan/7916153/working/building/REAL250005071794 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 931)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/931
`/scratch/stefan/7916153/working/3D/931' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071794.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071794.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071794/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071794 none NC(=O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 40, 52, 23, 40, 23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 52, 52, 23, 23, 23, 23, 23, 23, 1, 23, 23, 23, 23] 52
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: 146
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071794 none NC(=O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 14, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 15, 15, 1, 1, 1, 1, 1, 1, 23, 1, 1, 1, 1] 52
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 28])
total number of confs: 74
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071794 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071794
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071794/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071794
Building REAL250005071795
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071795'
/scratch/stefan/7916153/working/building/REAL250005071795 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071795

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071795/0 /scratch/stefan/7916153/working/building/REAL250005071795 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 932)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/932
`/scratch/stefan/7916153/working/3D/932' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071795.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071795.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071795/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071795 none CC(C)(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 11, 11, 11, 11] 11
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: 22
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071795 none CC(C)(C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1] 11
rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 40, 19, 20, 39, 38, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 26
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071795 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071795
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071795/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071795
Building REAL250005071796
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071796'
/scratch/stefan/7916153/working/building/REAL250005071796 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071796

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071796/0 /scratch/stefan/7916153/working/building/REAL250005071796 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 933)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/933
`/scratch/stefan/7916153/working/3D/933' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)N2CCCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1)

`REAL250005071796.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071796.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071796/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071796 none CC1(C(=O)N2CCCN(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', '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, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 5, 5, 5] 31
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 34, 17, 18, 24, 25, 26, 27, 28, 29, 31] set([0, 1, 3, 36, 37, 35, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 38, 30])
total number of confs: 39
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071796 none CC1(C(=O)N2CCCN(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', '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, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 19, 19, 31, 31, 31, 31, 31, 5, 5, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 31, 5, 5, 5, 5, 1, 1, 1, 1] 31
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: 74
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071796 none CC1(C(=O)N2CCCN(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', '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, 1, 11, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [31, 31, 15, 31, 15, 15, 15, 15, 10, 1, 10, 1, 1, 1, 1, 1, 1, 15, 15, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 1, 15, 15, 15, 15, 31, 31, 31, 31] 31
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: 81
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071796 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071796
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071796/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071796
Building REAL250005071797
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071797'
/scratch/stefan/7916153/working/building/REAL250005071797 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071797

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071797/0 /scratch/stefan/7916153/working/building/REAL250005071797 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 934)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/934
`/scratch/stefan/7916153/working/3D/934' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071797.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071797.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071797/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071797 none C[C@@H]1C[C@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 19, 19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 30, 1, 1, 1, 1] 72
rigid atoms, others: [32, 33, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 21, 22, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 34, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27])
total number of confs: 92
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071797 none C[C@@H]1C[C@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 7, 7, 19, 19, 19, 19, 19, 51, 51, 72, 72, 72, 72, 72, 19, 19, 2, 2, 2, 1, 1, 19, 19, 19, 19, 19, 19, 72, 19, 19, 19, 19] 72
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: 171
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071797 none C[C@@H]1C[C@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 60, 72, 30, 60, 30, 30, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 30, 72, 72, 72, 72, 72, 30, 30, 30, 30, 30, 30, 1, 30, 30, 30, 30] 72
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: 188
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071797 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071797
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071797/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071797
Building REAL250005071798
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071798'
/scratch/stefan/7916153/working/building/REAL250005071798 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071798

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071798/0 /scratch/stefan/7916153/working/building/REAL250005071798 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 935)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/935
`/scratch/stefan/7916153/working/3D/935' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071798.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071798.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071798/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071798 none CCC(F)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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, 53, 75, 25, 53, 25, 25, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 75, 75, 75, 75, 75, 75, 25, 25, 25, 25, 25, 25, 1, 25, 25, 25, 25] 75
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: 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071798 none CCC(F)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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: [23, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 23, 23, 23, 23, 23, 13, 1, 1, 1, 1, 1, 1, 25, 1, 1, 1, 1] 75
rigid atoms, others: [32, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 33, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26])
total number of confs: 144
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071798 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071798
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071798/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071798
Building REAL250005071799
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071799'
/scratch/stefan/7916153/working/building/REAL250005071799 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071799

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071799/0 /scratch/stefan/7916153/working/building/REAL250005071799 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 936)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/936
`/scratch/stefan/7916153/working/3D/936' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCF)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071799.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071799.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071799/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071799 none O=C(CCCF)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 8, 5, 5, 5, 8, 1, 11, 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
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [70, 29, 70, 132, 155, 158, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 132, 132, 158, 158, 158, 158, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 158
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: 643
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071799 none O=C(CCCF)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 8, 5, 5, 5, 8, 1, 11, 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
158  conformations in input
total number of sets (complete confs): 158
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 20, 32, 55, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 20, 20, 33, 33, 55, 54, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 158
rigid atoms, others: [32, 1, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30, 31] set([0, 33, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26])
total number of confs: 301
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071799 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071799
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071799/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071799
Building REAL250005071800
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071800'
/scratch/stefan/7916153/working/building/REAL250005071800 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071800

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071800/0 /scratch/stefan/7916153/working/building/REAL250005071800 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 937)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/937
`/scratch/stefan/7916153/working/3D/937' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1C[C@@H]1C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071800.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071800.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071800/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071800 none C[C@H]1C[C@@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 20, 7, 20, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 28, 1, 1, 1, 1] 78
rigid atoms, others: [32, 33, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 21, 22, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 34, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27])
total number of confs: 94
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071800 none C[C@H]1C[C@@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 20, 53, 53, 78, 78, 78, 78, 78, 20, 20, 2, 2, 2, 1, 1, 20, 20, 20, 20, 20, 20, 78, 20, 20, 20, 20] 78
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: 180
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071800 none C[C@H]1C[C@@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 56, 78, 28, 56, 28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 78, 78, 78, 78, 78, 28, 28, 28, 28, 28, 28, 1, 28, 28, 28, 28] 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, 37, 38])
total number of confs: 224
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071800 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071800
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071800/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071800
Building REAL250005071801
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071801'
/scratch/stefan/7916153/working/building/REAL250005071801 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071801

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071801/0 /scratch/stefan/7916153/working/building/REAL250005071801 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 938)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/938
`/scratch/stefan/7916153/working/3D/938' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071801.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071801.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071801/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071801 none O=C(CO)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 12, 8, 5, 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]
dock color type numbers: [6, 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]
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, 29, 52, 59, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 59, 59, 177, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 177
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: 346
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071801 none O=C(CO)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 12, 8, 5, 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]
dock color type numbers: [6, 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]
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, 1, 6, 14, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 14, 14, 42, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 177
rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 17, 18, 22, 23, 24, 25, 26, 27, 29, 30, 31] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 28])
total number of confs: 130
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071801 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071801
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071801/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071801
Building REAL250005071802
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071802'
/scratch/stefan/7916153/working/building/REAL250005071802 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071802

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071802/0 /scratch/stefan/7916153/working/building/REAL250005071802 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 939)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/939
`/scratch/stefan/7916153/working/3D/939' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCCN(C(=O)C2CCO2)CC1)

`REAL250005071802.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071802.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071802/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071802 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 7, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 1, 1, 18, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 1] 41
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 28, 29, 30, 31])
total number of confs: 66
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071802 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 18, 34, 34, 41, 41, 41, 18, 18, 1, 18, 18, 18, 18, 18, 18, 41, 41, 41, 41, 41, 18, 18, 18, 18] 41
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: 112
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071802 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [31, 13, 31, 41, 41, 41, 41, 41, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 1, 13, 13, 41, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 13, 13, 13, 13] 41
rigid atoms, others: [32, 13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36])
total number of confs: 94
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071802 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071802
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071802/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071802
Building REAL250005071803
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071803'
/scratch/stefan/7916153/working/building/REAL250005071803 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071803

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071803/0 /scratch/stefan/7916153/working/building/REAL250005071803 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 940)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/940
`/scratch/stefan/7916153/working/3D/940' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCCN(C(=O)C2COC2)CC1)

`REAL250005071803.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071803.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071803/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071803 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 1, 1, 28, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 1, 1, 1, 1] 57
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 28, 29, 30, 31])
total number of confs: 78
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071803 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 1, 10, 28, 28, 28, 28, 28, 48, 48, 57, 57, 57, 28, 28, 1, 28, 28, 28, 28, 28, 28, 57, 57, 57, 57, 57, 28, 28, 28, 28] 57
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: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071803 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 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, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [45, 14, 45, 57, 57, 57, 57, 57, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 1, 14, 14, 57, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 14, 14, 14, 14] 57
rigid atoms, others: [32, 13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36])
total number of confs: 136
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071803 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071803
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071803/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071803
Building REAL250005071804
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071804'
/scratch/stefan/7916153/working/building/REAL250005071804 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071804

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071804/0 /scratch/stefan/7916153/working/building/REAL250005071804 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 941)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/941
`/scratch/stefan/7916153/working/3D/941' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCO)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071804.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071804.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071804/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071804 none O=C(C=CCO)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 12, 8, 5, 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]
dock color type numbers: [6, 7, 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]
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: [72, 31, 72, 131, 131, 136, 31, 31, 31, 31, 10, 1, 10, 1, 1, 1, 1, 1, 1, 31, 31, 131, 131, 136, 136, 408, 31, 31, 31, 31, 31, 31, 1, 31, 31, 31, 31] 408
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: 798
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071804 none O=C(C=CCO)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 12, 8, 5, 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]
dock color type numbers: [6, 7, 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]
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: [6, 1, 6, 26, 26, 70, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 26, 26, 70, 70, 210, 1, 1, 1, 1, 1, 1, 31, 1, 1, 1, 1] 408
rigid atoms, others: [1, 34, 35, 36, 33, 6, 7, 8, 9, 10, 11, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25])
total number of confs: 499
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071804 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071804
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071804/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071804
Building REAL250005071805
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071805'
/scratch/stefan/7916153/working/building/REAL250005071805 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071805

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071805/0 /scratch/stefan/7916153/working/building/REAL250005071805 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 942)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/942
`/scratch/stefan/7916153/working/3D/942' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071805.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071805.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071805/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071805 none CCC=CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [140, 121, 121, 78, 31, 78, 31, 31, 31, 31, 10, 1, 10, 1, 1, 1, 1, 1, 1, 31, 31, 140, 140, 140, 140, 140, 121, 121, 31, 31, 31, 31, 31, 31, 1, 31, 31, 31, 31] 140
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: 451
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071805 none CCC=CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [51, 24, 24, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 51, 51, 51, 51, 51, 24, 24, 1, 1, 1, 1, 1, 1, 31, 1, 1, 1, 1] 140
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 246
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071805 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071805
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071805/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071805
Building REAL250005071806
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071806'
/scratch/stefan/7916153/working/building/REAL250005071806 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071806

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071806/0 /scratch/stefan/7916153/working/building/REAL250005071806 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 943)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/943
`/scratch/stefan/7916153/working/3D/943' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071806.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071806.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071806/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071806 none C#CCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [91, 91, 88, 59, 26, 59, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 91, 91, 91, 88, 88, 26, 26, 26, 26, 26, 26, 1, 26, 26, 26, 26] 91
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: 300
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071806 none C#CCCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 30, 30, 30, 18, 18, 1, 1, 1, 1, 1, 1, 26, 1, 1, 1, 1] 91
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25])
total number of confs: 169
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071806 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071806
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071806/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071806
Building REAL250005071807
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071807'
/scratch/stefan/7916153/working/building/REAL250005071807 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071807

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071807/0 /scratch/stefan/7916153/working/building/REAL250005071807 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 944)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/944
`/scratch/stefan/7916153/working/3D/944' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(O)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071807.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071807.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071807/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071807 none C=CC(O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 50, 62, 24, 50, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 62, 62, 62, 62, 186, 24, 24, 24, 24, 24, 24, 1, 24, 24, 24, 24] 186
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: 368
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071807 none C=CC(O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
186  conformations in input
total number of sets (complete confs): 186
using faster count positions algorithm for large data
unique positions, atoms: [33, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 33, 33, 33, 16, 48, 1, 1, 1, 1, 1, 1, 24, 1, 1, 1, 1] 186
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25])
total number of confs: 191
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071807 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071807
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071807/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071807
Building REAL250005071808
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071808'
/scratch/stefan/7916153/working/building/REAL250005071808 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071808

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071808/0 /scratch/stefan/7916153/working/building/REAL250005071808 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 945)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/945
`/scratch/stefan/7916153/working/3D/945' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071808.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071808.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071808/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071808 none CC(O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 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]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [54, 51, 54, 26, 51, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 54, 54, 54, 54, 162, 26, 26, 26, 26, 26, 26, 1, 26, 26, 26, 26] 162
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: 301
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071808 none CC(O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 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]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 18, 18, 18, 18, 54, 1, 1, 1, 1, 1, 1, 26, 1, 1, 1, 1] 162
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 29, 30, 35] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31])
total number of confs: 159
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071808 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071808
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071808/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071808
Building REAL250005071809
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071809'
/scratch/stefan/7916153/working/building/REAL250005071809 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071809

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071809/0 /scratch/stefan/7916153/working/building/REAL250005071809 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 946)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/946
`/scratch/stefan/7916153/working/3D/946' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071809.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071809.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071809/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071809 none CC(=O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 11, 1, 11, 8, 5, 5, 5, 8, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [56, 43, 56, 24, 43, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 56, 56, 56, 24, 24, 24, 24, 24, 24, 1, 24, 24, 24, 24] 56
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: 160
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071809 none CC(=O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 11, 1, 11, 8, 5, 5, 5, 8, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 17, 17, 17, 1, 1, 1, 1, 1, 1, 24, 1, 1, 1, 1] 56
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 18, 19, 23, 24, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 29])
total number of confs: 82
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071809 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071809
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071809/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071809
Building REAL250005071810
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071810'
/scratch/stefan/7916153/working/building/REAL250005071810 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071810

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071810/0 /scratch/stefan/7916153/working/building/REAL250005071810 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 947)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/947
`/scratch/stefan/7916153/working/3D/947' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCCN(C(=O)C2(F)CC2)CC1)

`REAL250005071810.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071810.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071810/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071810 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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: [7, 1, 7, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 1, 1, 22, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 1, 1, 1, 1] 52
rigid atoms, others: [32, 1, 34, 35, 33, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 28, 29, 30, 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071810 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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: [10, 1, 1, 1, 1, 1, 1, 1, 10, 22, 22, 22, 22, 22, 33, 33, 52, 52, 52, 22, 22, 1, 22, 22, 22, 22, 22, 22, 52, 52, 52, 52, 22, 22, 22, 22] 52
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: 157
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071810 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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: [37, 15, 37, 52, 52, 52, 52, 52, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 15, 15, 52, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 15, 15, 15, 15] 52
rigid atoms, others: [13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 112
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071810 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071810
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071810/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071810
Building REAL250005071811
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071811'
/scratch/stefan/7916153/working/building/REAL250005071811 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071811

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071811/0 /scratch/stefan/7916153/working/building/REAL250005071811 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 948)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/948
`/scratch/stefan/7916153/working/3D/948' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(F)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071811.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071811.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071811/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071811 none CC=C(F)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 15, 1, 11, 8, 5, 5, 5, 8, 1, 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, 7, 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
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [96, 96, 67, 96, 26, 67, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 96, 96, 96, 96, 26, 26, 26, 26, 26, 26, 1, 26, 26, 26, 26] 96
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: 277
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071811 none CC=C(F)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 15, 1, 11, 8, 5, 5, 5, 8, 1, 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, 7, 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
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 7, 29, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 26, 1, 1, 1, 1] 96
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 31])
total number of confs: 110
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071811 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071811
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071811/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071811
Building REAL250005071812
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071812'
/scratch/stefan/7916153/working/building/REAL250005071812 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071812

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071812/0 /scratch/stefan/7916153/working/building/REAL250005071812 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 949)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/949
`/scratch/stefan/7916153/working/3D/949' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CO)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071812.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071812.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071812/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071812 none CC(CO)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 47, 52, 52, 24, 47, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 52, 52, 52, 52, 52, 52, 156, 24, 24, 24, 24, 24, 24, 1, 24, 24, 24, 24] 156
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: 302
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071812 none CC(CO)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 6, 12, 24, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 12, 12, 12, 12, 24, 24, 72, 1, 1, 1, 1, 1, 1, 24, 1, 1, 1, 1] 156
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 209
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071812 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071812
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071812/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071812
Building REAL250005071813
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071813'
/scratch/stefan/7916153/working/building/REAL250005071813 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071813

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071813/0 /scratch/stefan/7916153/working/building/REAL250005071813 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 950)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/950
`/scratch/stefan/7916153/working/3D/950' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCCN(C(=O)C2(O)CC2)CC1)

`REAL250005071813.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071813.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071813/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071813 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 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
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 1, 1, 20, 1, 1, 1, 1, 1, 1, 39, 13, 13, 13, 13, 1, 1, 1, 1] 144
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 28, 29, 30, 31])
total number of confs: 106
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071813 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 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
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 33, 33, 48, 48, 48, 20, 20, 1, 20, 20, 20, 20, 20, 20, 144, 48, 48, 48, 48, 20, 20, 20, 20] 144
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: 287
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071813 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 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
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [37, 13, 37, 48, 48, 48, 48, 48, 13, 13, 13, 13, 5, 1, 5, 1, 1, 1, 1, 13, 13, 48, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 13, 13, 13] 144
rigid atoms, others: [32, 13, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 115
number of broken/clashed sets: 34
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071813 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071813
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071813/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071813
Building REAL250005071814
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071814'
/scratch/stefan/7916153/working/building/REAL250005071814 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071814

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071814/0 /scratch/stefan/7916153/working/building/REAL250005071814 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 951)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/951
`/scratch/stefan/7916153/working/3D/951' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CCC1)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071814.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071814.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071814/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071814 none O=C(C1=CCC1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 8, 5, 5, 5, 8, 1, 11, 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
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [6, 1, 6, 12, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 22, 1, 1, 1, 1] 39
rigid atoms, others: [1, 34, 35, 36, 33, 6, 7, 8, 9, 10, 11, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25])
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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071814 none O=C(C1=CCC1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 8, 5, 5, 5, 8, 1, 11, 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
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [8, 1, 1, 1, 1, 1, 8, 12, 12, 12, 12, 12, 30, 30, 39, 39, 39, 39, 39, 12, 12, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 39, 12, 12, 12, 12] 39
rigid atoms, others: [1, 2, 3, 4, 5, 21, 22, 23, 24, 25] set([0, 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: 96
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071814 none O=C(C1=CCC1)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 8, 5, 5, 5, 8, 1, 11, 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
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [39, 22, 39, 39, 39, 39, 22, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 39, 39, 39, 39, 39, 22, 22, 22, 22, 22, 22, 1, 22, 22, 22, 22] 39
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: 90
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071814 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071814
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071814/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071814
Building REAL250005071815
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071815'
/scratch/stefan/7916153/working/building/REAL250005071815 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071815

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071815/0 /scratch/stefan/7916153/working/building/REAL250005071815 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 952)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/952
`/scratch/stefan/7916153/working/3D/952' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CF)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071815.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071815.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071815/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071815 none CC(CF)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [57, 50, 57, 63, 26, 50, 26, 26, 26, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 26, 57, 57, 57, 57, 63, 63, 26, 26, 26, 26, 26, 26, 1, 26, 26, 26, 26] 63
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: 190
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071815 none CC(CF)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 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
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [12, 6, 12, 26, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 12, 12, 12, 12, 26, 26, 1, 1, 1, 1, 1, 1, 26, 1, 1, 1, 1] 63
rigid atoms, others: [32, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 33, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26])
total number of confs: 139
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071815 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071815
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071815/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071815
Building REAL250005071816
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071816'
/scratch/stefan/7916153/working/building/REAL250005071816 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071816

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071816/0 /scratch/stefan/7916153/working/building/REAL250005071816 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 953)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/953
`/scratch/stefan/7916153/working/3D/953' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071816.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071816.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071816/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071816 none CC=CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 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
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 53, 29, 53, 29, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 62, 62, 62, 62, 62, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 62
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: 154
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071816 none CC=CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 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
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 62
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 29, 30, 35] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31])
total number of confs: 85
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071816 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071816
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071816/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071816
Building REAL250005071817
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071817'
/scratch/stefan/7916153/working/building/REAL250005071817 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071817

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071817/0 /scratch/stefan/7916153/working/building/REAL250005071817 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 954)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/954
`/scratch/stefan/7916153/working/3D/954' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCF)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071817.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071817.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071817/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071817 none O=C(C=CCF)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 1, 5, 15, 8, 5, 5, 5, 8, 1, 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, 7, 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
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [66, 29, 66, 96, 96, 100, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 96, 96, 100, 100, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 100
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: 284
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071817 none O=C(C=CCF)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 1, 5, 15, 8, 5, 5, 5, 8, 1, 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, 7, 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
100  conformations in input
total number of sets (complete confs): 100
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 27, 27, 60, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 27, 27, 60, 60, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 100
rigid atoms, others: [32, 1, 34, 35, 33, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 31])
total number of confs: 253
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071817 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071817
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071817/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071817
Building REAL250005071818
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071818'
/scratch/stefan/7916153/working/building/REAL250005071818 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL250005071818 as failed and skipping
/scratch/stefan/7916153/working /scratch/stefan/7916153
`/scratch/stefan/7916153/working/building/REAL250005071818' -> `/scratch/stefan/7916153/failed/REAL250005071818'
Building REAL250005071819
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071819'
/scratch/stefan/7916153/working/building/REAL250005071819 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071819

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071819/0 /scratch/stefan/7916153/working/building/REAL250005071819 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 955)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/955
`/scratch/stefan/7916153/working/3D/955' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071819.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071819.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071819/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071819 none C[C@H](O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 7, 12, 1, 11, 8, 5, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 44, 44, 23, 44, 23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 44, 44, 44, 132, 23, 23, 23, 23, 23, 23, 1, 23, 23, 23, 23] 132
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: 232
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071819 none C[C@H](O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 7, 12, 1, 11, 8, 5, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 7, 11, 11, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 11, 11, 11, 33, 1, 1, 1, 1, 1, 1, 23, 1, 1, 1, 1] 132
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 31])
total number of confs: 105
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071819 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071819
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071819/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071819
Building REAL250005071820
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071820'
/scratch/stefan/7916153/working/building/REAL250005071820 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071820

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071820/0 /scratch/stefan/7916153/working/building/REAL250005071820 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 956)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/956
`/scratch/stefan/7916153/working/3D/956' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071820.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071820.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071820/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071820 none CON=CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 43, 21, 43, 21, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 70, 70, 70, 70, 21, 21, 21, 21, 21, 21, 1, 21, 21, 21, 21] 70
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: 198
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071820 none CON=CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 27, 27, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 38, 38, 38, 27, 1, 1, 1, 1, 1, 1, 21, 1, 1, 1, 1] 70
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 31])
total number of confs: 123
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071820 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071820
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071820/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071820
Building REAL250005071821
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071821'
/scratch/stefan/7916153/working/building/REAL250005071821 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071821

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071821/0 /scratch/stefan/7916153/working/building/REAL250005071821 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 957)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/957
`/scratch/stefan/7916153/working/3D/957' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071821.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071821.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071821/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071821 none C[C@@H]1C[C@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 19, 19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 30, 1, 1, 1, 1] 72
rigid atoms, others: [32, 33, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 21, 22, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 34, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27])
total number of confs: 92
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071821 none C[C@@H]1C[C@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 7, 7, 19, 19, 19, 19, 19, 51, 51, 72, 72, 72, 72, 72, 19, 19, 2, 2, 2, 1, 1, 19, 19, 19, 19, 19, 19, 72, 19, 19, 19, 19] 72
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: 171
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071821 none C[C@@H]1C[C@H]1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 60, 72, 30, 60, 30, 30, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 30, 72, 72, 72, 72, 72, 30, 30, 30, 30, 30, 30, 1, 30, 30, 30, 30] 72
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: 188
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071821 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071821
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071821/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071821
Building REAL250005071822
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071822'
/scratch/stefan/7916153/working/building/REAL250005071822 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071822

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071822/0 /scratch/stefan/7916153/working/building/REAL250005071822 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 958)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/958
`/scratch/stefan/7916153/working/3D/958' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(O)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071822.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071822.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071822/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071822 none CC(C)(O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 28, 39, 39, 17, 28, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 39, 39, 39, 39, 39, 39, 117, 17, 17, 17, 17, 17, 17, 1, 17, 17, 17, 17] 117
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: 259
number of broken/clashed sets: 53
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071822 none CC(C)(O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 4, 6, 6, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 1, 1, 6, 6, 6, 6, 6, 6, 18, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1] 117
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 69
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071822 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071822
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071822/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071822
Building REAL250005071823
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071823'
/scratch/stefan/7916153/working/building/REAL250005071823 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071823

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071823/0 /scratch/stefan/7916153/working/building/REAL250005071823 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 959)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/959
`/scratch/stefan/7916153/working/3D/959' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071823.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071823.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071823/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071823 none C=C(C)CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 108, 64, 29, 64, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 108, 108, 108, 108, 108, 108, 108, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 108
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: 361
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071823 none C=C(C)CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 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
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [36, 24, 36, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 36, 36, 36, 36, 36, 24, 24, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 108
rigid atoms, others: [32, 33, 35, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 34])
total number of confs: 166
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071823 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071823
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071823/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071823
Building REAL250005071824
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071824'
/scratch/stefan/7916153/working/building/REAL250005071824 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071824

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071824/0 /scratch/stefan/7916153/working/building/REAL250005071824 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 960)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/960
`/scratch/stefan/7916153/working/3D/960' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071824.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071824.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071824/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071824 none C=CCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 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
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [94, 94, 61, 27, 61, 27, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 94, 94, 94, 94, 94, 27, 27, 27, 27, 27, 27, 1, 27, 27, 27, 27] 94
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: 320
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071824 none C=CCC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 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
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [41, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 41, 41, 41, 20, 20, 1, 1, 1, 1, 1, 1, 27, 1, 1, 1, 1] 94
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 29, 30, 35] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31])
total number of confs: 176
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071824 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071824
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071824/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071824
Building REAL250005071825
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071825'
/scratch/stefan/7916153/working/building/REAL250005071825 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005071825

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071825/0 /scratch/stefan/7916153/working/building/REAL250005071825 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 961)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/961
`/scratch/stefan/7916153/working/3D/961' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071825.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071825.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071825/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071825 none C[NH+](C)CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7] 7
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: 15
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071825 none C[NH+](C)CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 1, 1, 1, 1] 7
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 12, 40, 20, 21, 39, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 34
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071825 /scratch/stefan/7916153/working /scratch/stefan/7916153
mkdir: created directory `1'
/scratch/stefan/7916153/working/building/REAL250005071825/1 /scratch/stefan/7916153/working/building/REAL250005071825 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 1 (index: 962)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/962
`/scratch/stefan/7916153/working/3D/962' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071825.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005071825.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071825/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071825 none CN(C)CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 62, 29, 62, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 103, 103, 103, 103, 103, 103, 99, 99, 29, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 103
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: 350
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071825 none CN(C)CC(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 23, 36, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 36, 36, 36, 36, 36, 36, 23, 23, 1, 1, 1, 1, 1, 1, 29, 1, 1, 1, 1] 103
rigid atoms, others: [32, 33, 34, 4, 37, 6, 7, 8, 9, 10, 11, 19, 20, 39, 36, 38, 29, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 35, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 170
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071825 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071825
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
1: /scratch/stefan/7916153/working/building/REAL250005071825/1.*
0: /scratch/stefan/7916153/working/building/REAL250005071825/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071825
Building REAL250005071826
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071826'
/scratch/stefan/7916153/working/building/REAL250005071826 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071826

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071826/0 /scratch/stefan/7916153/working/building/REAL250005071826 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 963)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/963
`/scratch/stefan/7916153/working/3D/963' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071826.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071826.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071826/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071826 none N#CCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1 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', '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, 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, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 51, 23, 51, 23, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 75, 75, 23, 23, 23, 23, 23, 23, 1, 23, 23, 23, 23] 75
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: 251
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071826 none N#CCC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1 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', '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, 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, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 22, 22, 1, 1, 1, 1, 1, 1, 23, 1, 1, 1, 1] 75
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 28])
total number of confs: 112
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071826 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071826
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071826/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071826
Building REAL250005071827
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071827'
/scratch/stefan/7916153/working/building/REAL250005071827 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071827

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071827/0 /scratch/stefan/7916153/working/building/REAL250005071827 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 964)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/964
`/scratch/stefan/7916153/working/3D/964' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCCN(C(=O)C2CC2F)CC1)

`REAL250005071827.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071827.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071827/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071827 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', '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', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 1, 1, 28, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 1, 1, 1, 1] 63
rigid atoms, others: [32, 1, 34, 35, 33, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 28, 29, 30, 31])
total number of confs: 87
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071827 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', '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', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 1, 10, 28, 28, 28, 28, 28, 45, 45, 63, 63, 63, 28, 28, 1, 28, 28, 28, 28, 28, 28, 63, 63, 63, 63, 28, 28, 28, 28] 63
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: 179
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071827 none O=C(C1=CC(=O)[N-]O1)N1CCCN(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', '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', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 5, 8, 1, 11, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [44, 18, 44, 63, 63, 63, 63, 63, 18, 18, 18, 18, 8, 1, 8, 1, 1, 1, 1, 18, 18, 63, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 18, 18, 18, 18] 63
rigid atoms, others: [13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 141
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071827 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071827
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071827/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071827
Building REAL250005071828
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071828'
/scratch/stefan/7916153/working/building/REAL250005071828 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071828

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071828/0 /scratch/stefan/7916153/working/building/REAL250005071828 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 965)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/965
`/scratch/stefan/7916153/working/3D/965' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071828.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071828.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071828/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071828 none O=C(CCF)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 15, 8, 5, 5, 5, 8, 1, 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
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [46, 23, 46, 78, 78, 23, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 78, 78, 78, 78, 23, 23, 23, 23, 23, 23, 1, 23, 23, 23, 23] 78
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: 275
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071828 none O=C(CCF)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 15, 8, 5, 5, 5, 8, 1, 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
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 13, 27, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 13, 13, 27, 27, 1, 1, 1, 1, 1, 1, 23, 1, 1, 1, 1] 78
rigid atoms, others: [32, 1, 34, 33, 5, 6, 7, 8, 9, 10, 18, 19, 24, 25, 26, 27, 28, 29, 31] set([0, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 30])
total number of confs: 149
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071828 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071828
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071828/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071828
Building REAL250005071829
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071829'
/scratch/stefan/7916153/working/building/REAL250005071829 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071829

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071829/0 /scratch/stefan/7916153/working/building/REAL250005071829 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 966)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/966
`/scratch/stefan/7916153/working/3D/966' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CO[C@H](C)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071829.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071829.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071829/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071829 none CO[C@H](C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 37, 28, 37, 37, 18, 28, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 18, 45, 45, 45, 37, 37, 37, 18, 18, 18, 18, 18, 18, 1, 18, 18, 18, 18] 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, 37, 38])
total number of confs: 135
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071829 none CO[C@H](C)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 11, 7, 11, 11, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 1, 1, 15, 15, 15, 11, 11, 11, 1, 1, 1, 1, 1, 1, 18, 1, 1, 1, 1] 45
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 34, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27])
total number of confs: 74
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071829 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071829
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071829/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071829
Building REAL250005071830
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071830'
/scratch/stefan/7916153/working/building/REAL250005071830 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071830

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071830/0 /scratch/stefan/7916153/working/building/REAL250005071830 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 967)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/967
`/scratch/stefan/7916153/working/3D/967' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071830.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071830.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071830/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071830 none C[C@@H](O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 7, 12, 1, 11, 8, 5, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 31, 33, 33, 19, 31, 19, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 33, 33, 33, 99, 19, 19, 19, 19, 19, 19, 1, 19, 19, 19, 19] 99
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: 185
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071830 none C[C@@H](O)C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.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, 7, 12, 1, 11, 8, 5, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 6, 10, 10, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 10, 10, 10, 30, 1, 1, 1, 1, 1, 1, 19, 1, 1, 1, 1] 99
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 31])
total number of confs: 95
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071830 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071830
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071830/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071830
Building REAL250005071831
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071831'
/scratch/stefan/7916153/working/building/REAL250005071831 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071831

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071831/0 /scratch/stefan/7916153/working/building/REAL250005071831 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 968)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/968
`/scratch/stefan/7916153/working/3D/968' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071831.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071831.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071831/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071831 none C=C1CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 19, 1, 1, 1, 1] 62
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25])
total number of confs: 83
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071831 none C=C1CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 20, 50, 50, 62, 62, 62, 62, 62, 20, 20, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 62, 20, 20, 20, 20] 62
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: 144
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071831 none C=C1CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 42, 19, 42, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 62, 62, 62, 62, 62, 19, 19, 19, 19, 19, 19, 1, 19, 19, 19, 19] 62
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: 184
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071831 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071831
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071831/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071831
Building REAL250005071832
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071832'
/scratch/stefan/7916153/working/building/REAL250005071832 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071832

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071832/0 /scratch/stefan/7916153/working/building/REAL250005071832 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 969)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/969
`/scratch/stefan/7916153/working/3D/969' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071832.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071832.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071832/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071832 none CC1=CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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: [20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 27, 1, 1, 1, 1] 72
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 19, 20, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25])
total number of confs: 91
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071832 none CC1=CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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, 20, 20, 20, 20, 20, 54, 54, 72, 72, 72, 72, 72, 20, 20, 2, 2, 2, 1, 1, 20, 20, 20, 20, 20, 20, 72, 20, 20, 20, 20] 72
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: 172
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071832 none CC1=CC1C(=O)N1CCCN(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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 5, 8, 1, 11, 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, 7, 6, 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, 56, 27, 56, 27, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 72, 72, 72, 72, 72, 27, 27, 27, 27, 27, 27, 1, 27, 27, 27, 27] 72
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: 198
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071832 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071832
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071832/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071832
Building REAL250005071833
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071833'
/scratch/stefan/7916153/working/building/REAL250005071833 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071833

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071833/0 /scratch/stefan/7916153/working/building/REAL250005071833 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 970)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/970
`/scratch/stefan/7916153/working/3D/970' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005071833.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071833.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071833/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071833 none C=CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1 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', '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, 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, 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
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [44, 44, 21, 44, 21, 21, 21, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 44, 44, 44, 21, 21, 21, 21, 21, 21, 1, 21, 21, 21, 21] 44
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: 113
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071833 none C=CC(=O)N1CCCN(C(=O)C2=CC(=O)[N-]O2)CC1 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', '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, 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, 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
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 17, 17, 17, 1, 1, 1, 1, 1, 1, 21, 1, 1, 1, 1] 44
rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 17, 18, 22, 23, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 28])
total number of confs: 75
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071833 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071833
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071833/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071833
Building REAL250005071834
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071834'
/scratch/stefan/7916153/working/building/REAL250005071834 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071834

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071834/0 /scratch/stefan/7916153/working/building/REAL250005071834 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 971)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/971
`/scratch/stefan/7916153/working/3D/971' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071834.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071834.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071834/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071834 none CCC(=O)NC1(C)CN(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 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]
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, 24, 24, 24, 17, 17, 17, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 40, 40, 40, 40, 40, 24, 17, 17, 17, 17, 16, 1, 17, 17] 40
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: 154
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071834 none CCC(=O)NC1(C)CN(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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 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]
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: [14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 14, 14, 14, 14, 14, 3, 2, 2, 2, 1, 1, 17, 1, 1] 40
rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 27, 28, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29])
total number of confs: 81
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071834 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071834
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071834/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071834
Building REAL250005071835
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071835'
/scratch/stefan/7916153/working/building/REAL250005071835 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071835

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071835/0 /scratch/stefan/7916153/working/building/REAL250005071835 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 972)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/972
`/scratch/stefan/7916153/working/3D/972' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071835.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071835.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071835/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071835 none COCCC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 3, 7, 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]
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, 72, 25, 25, 25, 23, 23, 23, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 85, 85, 85, 85, 85, 72, 72, 25, 23, 23, 23, 23, 22, 1, 23, 23] 85
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: 313
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071835 none COCCC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 3, 7, 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]
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: [42, 31, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 42, 42, 42, 31, 31, 19, 19, 3, 2, 2, 2, 1, 1, 23, 1, 1] 85
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 193
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071835 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071835
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071835/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071835
Building REAL250005071836
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071836'
/scratch/stefan/7916153/working/building/REAL250005071836 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071836

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071836/0 /scratch/stefan/7916153/working/building/REAL250005071836 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 973)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/973
`/scratch/stefan/7916153/working/3D/973' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(NC(=O)C2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071836.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071836.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071836/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071836 none CC1(NC(=O)C2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 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]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [23, 13, 13, 1, 13, 1, 1, 1, 23, 23, 23, 52, 52, 62, 62, 62, 62, 62, 23, 23, 23, 23, 13, 1, 1, 1, 1, 1, 23, 23, 62, 23, 23] 62
rigid atoms, others: [3, 5, 6, 7, 23, 24, 25, 26, 27] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32])
total number of confs: 180
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071836 none CC1(NC(=O)C2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 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]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 23, 23, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 2, 2, 2, 3, 23, 23, 23, 23, 23, 1, 1, 17, 1, 1] 62
rigid atoms, others: [0, 1, 2, 32, 8, 9, 10, 18, 28, 29, 31] set([3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071836 none CC1(NC(=O)C2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 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]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 26, 26, 26, 62, 62, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 26, 62, 62, 62, 62, 62, 17, 17, 1, 17, 17] 62
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: 176
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071836 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071836
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071836/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071836
Building REAL250005071837
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071837'
/scratch/stefan/7916153/working/building/REAL250005071837 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071837

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071837/0 /scratch/stefan/7916153/working/building/REAL250005071837 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 974)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/974
`/scratch/stefan/7916153/working/3D/974' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(NC(=O)C2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071837.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071837.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071837/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071837 none CC1(NC(=O)C2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 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, 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]
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: [21, 12, 12, 1, 12, 1, 1, 1, 1, 21, 21, 21, 61, 61, 73, 73, 73, 73, 73, 21, 21, 21, 21, 12, 1, 1, 1, 1, 1, 1, 1, 21, 21, 73, 21, 21] 73
rigid atoms, others: [3, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35])
total number of confs: 198
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071837 none CC1(NC(=O)C2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 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, 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]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 21, 21, 21, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 21, 21, 21, 21, 21, 21, 21, 1, 1, 22, 1, 1] 73
rigid atoms, others: [0, 1, 2, 35, 32, 9, 10, 11, 34, 19, 31] set([3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 87
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071837 none CC1(NC(=O)C2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 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, 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]
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: [22, 22, 22, 34, 34, 34, 73, 73, 73, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 34, 73, 73, 73, 73, 73, 73, 73, 22, 22, 1, 22, 22] 73
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: 211
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071837 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071837
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071837/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071837
Building REAL250005071838
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071838'
/scratch/stefan/7916153/working/building/REAL250005071838 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071838

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071838/0 /scratch/stefan/7916153/working/building/REAL250005071838 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 975)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/975
`/scratch/stefan/7916153/working/3D/975' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(NC(=O)C2CCCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071838.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071838.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071838/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071838 none CC1(NC(=O)C2CCCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 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, 4, 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]
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: [19, 11, 11, 1, 11, 1, 1, 1, 1, 1, 19, 19, 19, 55, 55, 69, 69, 69, 69, 69, 19, 19, 19, 19, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 69, 19, 19] 69
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38])
total number of confs: 180
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071838 none CC1(NC(=O)C2CCCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 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, 4, 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]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 19, 19, 19, 19, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 23, 1, 1] 69
rigid atoms, others: [0, 1, 2, 35, 37, 38, 10, 11, 12, 34, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 85
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071838 none CC1(NC(=O)C2CCCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 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, 4, 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]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 33, 33, 33, 69, 69, 69, 69, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 33, 69, 69, 69, 69, 69, 69, 69, 69, 69, 23, 22, 1, 23, 23] 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: 194
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071838 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071838
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071838/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071838
Building REAL250005071839
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071839'
/scratch/stefan/7916153/working/building/REAL250005071839 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071839

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071839/0 /scratch/stefan/7916153/working/building/REAL250005071839 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 976)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/976
`/scratch/stefan/7916153/working/3D/976' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(NC(=O)CC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071839.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071839.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071839/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071839 none CC1(NC(=O)CC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 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, 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]
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: [36, 22, 22, 3, 22, 1, 1, 1, 1, 36, 36, 36, 98, 98, 128, 128, 128, 128, 128, 36, 36, 36, 36, 22, 3, 3, 1, 1, 1, 1, 1, 36, 36, 128, 36, 36] 128
rigid atoms, others: [5, 6, 7, 8, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35])
total number of confs: 344
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071839 none CC1(NC(=O)CC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 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, 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]
0  hydrogens need rotated
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 22, 36, 36, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 2, 2, 2, 3, 22, 22, 36, 36, 36, 36, 36, 1, 1, 20, 1, 1] 128
rigid atoms, others: [0, 1, 2, 35, 32, 9, 10, 11, 34, 19, 31] set([3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 164
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071839 none CC1(NC(=O)CC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 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, 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]
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: [20, 20, 20, 32, 32, 32, 92, 128, 128, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 32, 92, 92, 128, 128, 128, 128, 128, 20, 20, 1, 20, 20] 128
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: 487
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071839 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071839
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071839/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071839
Building REAL250005071840
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071840'
/scratch/stefan/7916153/working/building/REAL250005071840 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071840

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071840/0 /scratch/stefan/7916153/working/building/REAL250005071840 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 977)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/977
`/scratch/stefan/7916153/working/3D/977' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071840.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071840.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071840/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071840 none CC(C)(F)C(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 25, 57, 57, 25, 25, 18, 18, 18, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 57, 57, 57, 57, 57, 57, 25, 18, 18, 18, 17, 18, 1, 18, 18] 57
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: 203
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071840 none CC(C)(F)C(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [19, 3, 19, 19, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 19, 19, 19, 19, 19, 19, 3, 2, 2, 2, 1, 1, 18, 1, 1] 57
rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32])
total number of confs: 96
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071840 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071840
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071840/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071840
Building REAL250005071841
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071841'
/scratch/stefan/7916153/working/building/REAL250005071841 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071841

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071841/0 /scratch/stefan/7916153/working/building/REAL250005071841 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 978)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/978
`/scratch/stefan/7916153/working/3D/978' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(F)(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071841.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071841.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071841/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071841 none CC(F)(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 23, 69, 69, 23, 23, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 69, 69, 69, 23, 15, 15, 15, 15, 15, 1, 15, 15] 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: 244
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071841 none CC(F)(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 15, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [23, 3, 23, 23, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 23, 23, 23, 3, 2, 2, 2, 1, 1, 15, 1, 1] 69
rigid atoms, others: [6, 7, 8, 9, 10, 11, 19, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29])
total number of confs: 103
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071841 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071841
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071841/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071841
Building REAL250005071842
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071842'
/scratch/stefan/7916153/working/building/REAL250005071842 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071842

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071842/0 /scratch/stefan/7916153/working/building/REAL250005071842 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 979)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/979
`/scratch/stefan/7916153/working/3D/979' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071842.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071842.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071842/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071842 none COCC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 3, 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]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 27, 27, 27, 24, 24, 24, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 53, 53, 53, 53, 53, 27, 24, 24, 24, 24, 24, 1, 24, 24] 53
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: 177
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071842 none COCC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 3, 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]
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: [30, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 30, 30, 30, 17, 17, 3, 2, 2, 2, 1, 1, 24, 1, 1] 53
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30])
total number of confs: 118
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071842 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071842
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071842/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071842
Building REAL250005071843
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071843'
/scratch/stefan/7916153/working/building/REAL250005071843 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071843

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071843/0 /scratch/stefan/7916153/working/building/REAL250005071843 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 980)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/980
`/scratch/stefan/7916153/working/3D/980' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071843.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071843.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071843/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071843 none CCCC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 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]
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, 80, 35, 35, 35, 24, 24, 24, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 90, 90, 90, 90, 90, 80, 80, 35, 24, 24, 24, 24, 23, 1, 24, 24] 90
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: 349
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071843 none CCCC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 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]
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: [26, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 33, 33, 33, 33, 33, 19, 19, 3, 2, 2, 2, 1, 1, 24, 1, 1] 90
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32])
total number of confs: 216
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071843 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071843
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071843/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071843
Building REAL250005071844
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071844'
/scratch/stefan/7916153/working/building/REAL250005071844 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071844

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071844/0 /scratch/stefan/7916153/working/building/REAL250005071844 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 981)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/981
`/scratch/stefan/7916153/working/3D/981' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(NC(=O)C2=CC=CO2)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071844.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071844.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071844/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071844 none CC1(NC(=O)C2=CC=CO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 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
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 13, 13, 13, 28, 28, 32, 32, 32, 32, 32, 13, 13, 13, 13, 8, 1, 1, 1, 13, 13, 32, 13, 13] 32
rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32])
total number of confs: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071844 none CC1(NC(=O)C2=CC=CO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 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
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 1, 2, 2, 2, 3, 13, 13, 13, 1, 1, 16, 1, 1] 32
rigid atoms, others: [0, 1, 2, 32, 10, 11, 12, 20, 28, 29, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30])
total number of confs: 50
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071844 none CC1(NC(=O)C2=CC=CO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 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
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [16, 16, 16, 23, 23, 23, 32, 32, 32, 32, 16, 9, 1, 9, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 23, 32, 32, 32, 16, 16, 1, 16, 16] 32
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: 72
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071844 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071844
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071844/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071844
Building REAL250005071845
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071845'
/scratch/stefan/7916153/working/building/REAL250005071845 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071845

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071845/0 /scratch/stefan/7916153/working/building/REAL250005071845 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 982)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/982
`/scratch/stefan/7916153/working/3D/982' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071845.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071845.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071845/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071845 none CC(=O)NCC(=O)NC1(C)CN(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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 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]
0  hydrogens need rotated
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [128, 128, 128, 119, 34, 34, 34, 28, 28, 28, 28, 11, 1, 11, 1, 1, 1, 1, 1, 1, 28, 128, 128, 128, 128, 119, 119, 34, 28, 28, 28, 28, 28, 1, 28, 28] 128
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: 413
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071845 none CC(=O)NCC(=O)NC1(C)CN(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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 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]
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: [69, 69, 69, 25, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 28, 28, 1, 69, 69, 69, 69, 25, 25, 3, 2, 2, 2, 1, 1, 28, 1, 1] 128
rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 253
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071845 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071845
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071845/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071845
Building REAL250005071846
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071846'
/scratch/stefan/7916153/working/building/REAL250005071846 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071846

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071846/0 /scratch/stefan/7916153/working/building/REAL250005071846 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 983)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/983
`/scratch/stefan/7916153/working/3D/983' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071846.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071846.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071846/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071846 none CC(C)CC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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]
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: [51, 52, 52, 21, 21, 21, 16, 16, 16, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 52, 52, 52, 52, 52, 52, 52, 52, 52, 21, 16, 16, 16, 16, 15, 1, 16, 16] 52
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: 193
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071846 none CC(C)CC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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]
0  hydrogens need rotated
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [16, 15, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 19, 19, 19, 19, 19, 19, 19, 15, 15, 3, 2, 2, 2, 1, 1, 16, 1, 1] 52
rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071846 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071846
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071846/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071846
Building REAL250005071847
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071847'
/scratch/stefan/7916153/working/building/REAL250005071847 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071847

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071847/0 /scratch/stefan/7916153/working/building/REAL250005071847 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 984)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/984
`/scratch/stefan/7916153/working/3D/984' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071847.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071847.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071847/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071847 none CC1CC1C(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 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]
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: [15, 15, 15, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 1, 1, 20, 1, 1] 53
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 73
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071847 none CC1CC1C(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 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]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 15, 44, 44, 53, 53, 53, 53, 53, 15, 2, 2, 2, 1, 1, 1, 1, 9, 15, 15, 15, 15, 15, 53, 15, 15] 53
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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071847 none CC1CC1C(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 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]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 53, 26, 26, 26, 20, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 53, 53, 53, 53, 53, 53, 53, 26, 20, 20, 20, 20, 20, 1, 20, 20] 53
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: 142
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071847 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071847
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071847/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071847
Building REAL250005071848
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071848'
/scratch/stefan/7916153/working/building/REAL250005071848 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071848

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071848/0 /scratch/stefan/7916153/working/building/REAL250005071848 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 985)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/985
`/scratch/stefan/7916153/working/3D/985' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071848.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071848.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071848/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071848 none CCOCC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 3, 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]
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, 80, 30, 30, 30, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 86, 86, 86, 86, 86, 80, 80, 30, 25, 25, 25, 25, 25, 1, 25, 25] 86
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: 268
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071848 none CCOCC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 3, 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]
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: [49, 45, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 49, 49, 49, 49, 49, 19, 19, 3, 2, 2, 2, 1, 1, 25, 1, 1] 86
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 166
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071848 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071848
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071848/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071848
Building REAL250005071849
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071849'
/scratch/stefan/7916153/working/building/REAL250005071849 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071849

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071849/0 /scratch/stefan/7916153/working/building/REAL250005071849 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 986)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/986
`/scratch/stefan/7916153/working/3D/986' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071849.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071849.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071849/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071849 none CC(C)=CC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 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]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [35, 35, 35, 22, 22, 22, 18, 18, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 18, 35, 35, 35, 35, 35, 35, 35, 22, 18, 18, 18, 18, 18, 1, 18, 18] 35
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: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071849 none CC(C)=CC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 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]
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: [11, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 11, 11, 11, 11, 11, 11, 11, 3, 2, 2, 2, 1, 1, 18, 1, 1] 35
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 63
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071849 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071849
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071849/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071849
Building REAL250005071850
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071850'
/scratch/stefan/7916153/working/building/REAL250005071850 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071850

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071850/0 /scratch/stefan/7916153/working/building/REAL250005071850 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 987)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/987
`/scratch/stefan/7916153/working/3D/987' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(NC(=O)C2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071850.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071850.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071850/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071850 none CC1(NC(=O)C2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [20, 11, 11, 1, 11, 1, 1, 1, 1, 1, 20, 20, 20, 54, 54, 64, 64, 64, 64, 64, 20, 20, 20, 20, 11, 1, 1, 1, 1, 1, 1, 1, 20, 20, 64, 20, 20] 64
rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36])
total number of confs: 179
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071850 none CC1(NC(=O)C2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 20, 20, 20, 20, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 20, 20, 20, 20, 20, 20, 20, 1, 1, 23, 1, 1] 64
rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34])
total number of confs: 86
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071850 none CC1(NC(=O)C2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 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
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 32, 32, 32, 64, 64, 64, 64, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 32, 64, 64, 64, 64, 64, 64, 64, 23, 23, 1, 23, 23] 64
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: 169
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071850 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071850
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071850/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071850
Building REAL250005071851
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071851'
/scratch/stefan/7916153/working/building/REAL250005071851 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071851

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071851/0 /scratch/stefan/7916153/working/building/REAL250005071851 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 988)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/988
`/scratch/stefan/7916153/working/3D/988' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071851.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071851.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071851/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071851 none CSCC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 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]
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, 82, 29, 29, 29, 23, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 94, 94, 94, 82, 82, 29, 23, 23, 23, 23, 23, 1, 23, 23] 94
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: 303
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071851 none CSCC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 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]
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: [49, 21, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 49, 49, 49, 21, 21, 3, 2, 2, 2, 1, 1, 23, 1, 1] 94
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30])
total number of confs: 151
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071851 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071851
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071851/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071851
Building REAL250005071852
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071852'
/scratch/stefan/7916153/working/building/REAL250005071852 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071852

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071852/0 /scratch/stefan/7916153/working/building/REAL250005071852 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 989)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/989
`/scratch/stefan/7916153/working/3D/989' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071852.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071852.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071852/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071852 none CSCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 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]
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, 93, 85, 28, 28, 28, 22, 22, 22, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 136, 136, 136, 93, 93, 85, 85, 28, 22, 22, 22, 22, 21, 1, 22, 22] 136
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: 408
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071852 none CSCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 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]
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: [74, 30, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 74, 74, 74, 30, 30, 18, 18, 3, 2, 2, 2, 1, 1, 22, 1, 1] 136
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 231
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071852 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071852
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071852/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071852
Building REAL250005071853
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071853'
/scratch/stefan/7916153/working/building/REAL250005071853 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071853

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071853/0 /scratch/stefan/7916153/working/building/REAL250005071853 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 990)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/990
`/scratch/stefan/7916153/working/3D/990' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071853.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071853.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071853/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071853 none CC(C)CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
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: [131, 128, 132, 122, 38, 38, 38, 26, 26, 26, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 132, 132, 131, 132, 132, 132, 132, 128, 128, 122, 122, 38, 26, 26, 26, 26, 25, 1, 26, 26] 132
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: 500
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071853 none CC(C)CCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
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: [35, 32, 41, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 41, 41, 35, 41, 41, 41, 41, 32, 32, 19, 19, 3, 2, 2, 2, 1, 1, 26, 1, 1] 132
rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 40, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 259
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071853 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071853
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071853/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071853
Building REAL250005071854
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071854'
/scratch/stefan/7916153/working/building/REAL250005071854 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071854

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071854/0 /scratch/stefan/7916153/working/building/REAL250005071854 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 991)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/991
`/scratch/stefan/7916153/working/3D/991' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(NC(=O)C2=CC=CN2)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071854.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071854.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071854/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071854 none CC1(NC(=O)C2=CC=CN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 15, 15, 15, 30, 30, 35, 35, 35, 35, 35, 15, 15, 15, 15, 9, 1, 1, 1, 1, 15, 15, 35, 15, 15] 35
rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33])
total number of confs: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071854 none CC1(NC(=O)C2=CC=CN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 1, 2, 2, 2, 3, 15, 15, 15, 15, 1, 1, 12, 1, 1] 35
rigid atoms, others: [0, 1, 2, 33, 32, 10, 11, 12, 20, 29, 30] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 48
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071854 none CC1(NC(=O)C2=CC=CN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 12, 20, 20, 20, 35, 35, 35, 35, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 20, 35, 35, 35, 35, 12, 11, 1, 12, 12] 35
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])
total number of confs: 81
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071854 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071854
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071854/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071854
Building REAL250005071855
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071855'
/scratch/stefan/7916153/working/building/REAL250005071855 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071855

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071855/0 /scratch/stefan/7916153/working/building/REAL250005071855 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 992)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/992
`/scratch/stefan/7916153/working/3D/992' -> `0.mol2'
Preparing input files

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

`REAL250005071855.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071855.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071855/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071855 none CC1(NC(=O)C2=COC=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 12, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 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
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 9, 9, 9, 30, 30, 38, 38, 38, 38, 38, 9, 9, 9, 9, 5, 1, 1, 1, 9, 9, 38, 9, 9] 38
rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071855 none CC1(NC(=O)C2=COC=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 12, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 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
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 2, 2, 2, 3, 9, 9, 9, 1, 1, 13, 1, 1] 38
rigid atoms, others: [0, 1, 2, 32, 10, 11, 12, 20, 28, 29, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071855 none CC1(NC(=O)C2=COC=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 12, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 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
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 21, 21, 21, 38, 38, 38, 38, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 21, 38, 38, 38, 13, 13, 1, 13, 13] 38
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: 89
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071855 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071855
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071855/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071855
Building REAL250005071856
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071856'
/scratch/stefan/7916153/working/building/REAL250005071856 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071856

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071856/0 /scratch/stefan/7916153/working/building/REAL250005071856 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 993)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/993
`/scratch/stefan/7916153/working/3D/993' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071856.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071856.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071856/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071856 none CCCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [194, 189, 138, 109, 25, 25, 25, 20, 20, 20, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 196, 201, 201, 201, 201, 189, 187, 149, 149, 109, 109, 25, 20, 20, 20, 20, 19, 1, 20, 20] 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: 941
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071856 none CCCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
0  hydrogens 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, 65, 32, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 98, 109, 109, 109, 109, 67, 66, 39, 39, 19, 19, 3, 2, 2, 2, 1, 1, 20, 1, 1] 201
rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 40, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 684
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071856 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071856
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071856/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071856
Building REAL250005071857
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071857'
/scratch/stefan/7916153/working/building/REAL250005071857 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071857

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071857/0 /scratch/stefan/7916153/working/building/REAL250005071857 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 994)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/994
`/scratch/stefan/7916153/working/3D/994' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071857.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071857.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071857/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071857 none CC(C)(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
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, 32, 33, 33, 21, 21, 21, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 32, 32, 21, 19, 19, 19, 19, 19, 1, 19, 19] 33
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: 103
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071857 none CC(C)(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
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, 9, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 3, 2, 2, 2, 1, 1, 19, 1, 1] 33
rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 40, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 83
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071857 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071857
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071857/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071857
Building REAL250005071858
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071858'
/scratch/stefan/7916153/working/building/REAL250005071858 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071858

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071858/0 /scratch/stefan/7916153/working/building/REAL250005071858 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 995)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/995
`/scratch/stefan/7916153/working/3D/995' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071858.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071858.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071858/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071858 none CCCCC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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]
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: [157, 144, 131, 36, 36, 36, 25, 25, 25, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 157, 160, 160, 160, 160, 145, 145, 131, 131, 36, 25, 25, 25, 25, 24, 1, 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])
total number of confs: 653
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071858 none CCCCC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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]
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: [66, 31, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 66, 71, 71, 65, 66, 38, 38, 19, 19, 3, 2, 2, 2, 1, 1, 25, 1, 1] 160
rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 399
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071858 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071858
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071858/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071858
Building REAL250005071859
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071859'
/scratch/stefan/7916153/working/building/REAL250005071859 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071859

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071859/0 /scratch/stefan/7916153/working/building/REAL250005071859 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 996)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/996
`/scratch/stefan/7916153/working/3D/996' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071859.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071859.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071859/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071859 none CC(C)C(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 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]
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, 26, 43, 26, 26, 19, 19, 19, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 43, 43, 43, 43, 43, 43, 43, 26, 19, 19, 19, 19, 18, 1, 19, 19] 43
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: 147
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071859 none CC(C)C(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 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]
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: [12, 3, 12, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 12, 12, 12, 12, 12, 12, 12, 3, 2, 2, 2, 1, 1, 19, 1, 1] 43
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32])
total number of confs: 78
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071859 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071859
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071859/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071859
Building REAL250005071860
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071860'
/scratch/stefan/7916153/working/building/REAL250005071860 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071860

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071860/0 /scratch/stefan/7916153/working/building/REAL250005071860 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 997)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/997
`/scratch/stefan/7916153/working/3D/997' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071860.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071860.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071860/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071860 none CCC(C)C(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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]
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, 69, 28, 69, 28, 28, 22, 22, 22, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 22, 79, 79, 79, 79, 79, 69, 69, 69, 69, 28, 22, 22, 22, 22, 21, 1, 22, 22] 79
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: 299
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071860 none CCC(C)C(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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, 7, 7]
dock color type numbers: [7, 7, 7, 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]
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: [29, 21, 3, 21, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 32, 32, 32, 32, 32, 21, 21, 21, 21, 3, 2, 2, 2, 1, 1, 22, 1, 1] 79
rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 191
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071860 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071860
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071860/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071860
Building REAL250005071861
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071861'
/scratch/stefan/7916153/working/building/REAL250005071861 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071861

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071861/0 /scratch/stefan/7916153/working/building/REAL250005071861 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 998)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/998
`/scratch/stefan/7916153/working/3D/998' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071861.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071861.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071861/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071861 none CCC(CC)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
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: [40, 33, 16, 33, 39, 16, 16, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 40, 40, 40, 40, 40, 33, 39, 39, 39, 39, 39, 16, 14, 14, 14, 14, 13, 1, 14, 14] 41
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: 181
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071861 none CCC(CC)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
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: [16, 11, 3, 11, 14, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 14, 1, 16, 16, 16, 16, 16, 11, 14, 14, 14, 14, 14, 3, 2, 2, 2, 1, 1, 14, 1, 1] 41
rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 40, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 116
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071861 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071861
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071861/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071861
Building REAL250005071862
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071862'
/scratch/stefan/7916153/working/building/REAL250005071862 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071862

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071862/0 /scratch/stefan/7916153/working/building/REAL250005071862 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 999)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/999
`/scratch/stefan/7916153/working/3D/999' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(NC(=O)C2=CC=NN2)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071862.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071862.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071862/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071862 none CC1(NC(=O)C2=CC=NN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 30, 30, 30, 30, 30, 13, 13, 13, 13, 7, 1, 1, 1, 13, 13, 30, 13, 13] 30
rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32])
total number of confs: 87
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071862 none CC1(NC(=O)C2=CC=NN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 1, 2, 2, 2, 3, 13, 13, 13, 1, 1, 12, 1, 1] 30
rigid atoms, others: [0, 1, 2, 32, 10, 11, 12, 20, 28, 29, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30])
total number of confs: 46
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071862 none CC1(NC(=O)C2=CC=NN2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 12, 18, 18, 18, 30, 30, 30, 30, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 18, 30, 30, 30, 12, 12, 1, 12, 12] 30
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: 64
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071862 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071862
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071862/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071862
Building REAL250005071863
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071863'
/scratch/stefan/7916153/working/building/REAL250005071863 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071863

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071863/0 /scratch/stefan/7916153/working/building/REAL250005071863 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1000)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1000
`/scratch/stefan/7916153/working/3D/1000' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071863.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071863.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071863/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071863 none CSC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 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]
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, 78, 29, 78, 29, 29, 24, 24, 24, 24, 11, 1, 11, 1, 1, 1, 1, 1, 1, 24, 93, 93, 93, 78, 78, 78, 78, 29, 24, 24, 24, 24, 24, 1, 24, 24] 93
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: 293
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071863 none CSC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 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]
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: [47, 20, 3, 20, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 47, 47, 47, 20, 20, 20, 20, 3, 2, 2, 2, 1, 1, 24, 1, 1] 93
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 146
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071863 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071863
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071863/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071863
Building REAL250005071864
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071864'
/scratch/stefan/7916153/working/building/REAL250005071864 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071864

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071864/0 /scratch/stefan/7916153/working/building/REAL250005071864 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1001)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1001
`/scratch/stefan/7916153/working/3D/1001' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071864.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071864.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071864/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071864 none CCOC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 3, 7, 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]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 61, 29, 61, 29, 29, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 63, 63, 63, 63, 63, 61, 61, 61, 61, 29, 24, 24, 24, 24, 24, 1, 24, 24] 63
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: 206
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071864 none CCOC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 3, 7, 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]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 19, 3, 19, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 33, 33, 33, 33, 33, 19, 19, 19, 19, 3, 2, 2, 2, 1, 1, 24, 1, 1] 63
rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 128
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071864 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071864
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071864/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071864
Building REAL250005071865
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071865'
/scratch/stefan/7916153/working/building/REAL250005071865 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071865

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071865/0 /scratch/stefan/7916153/working/building/REAL250005071865 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1002)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1002
`/scratch/stefan/7916153/working/3D/1002' -> `0.mol2'
Preparing input files

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

`REAL250005071865.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071865.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071865/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071865 none CC1(NC(=O)C2=CNN=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 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]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 21, 21, 21, 21, 21, 5, 5, 5, 5, 3, 1, 1, 1, 5, 5, 21, 5, 5] 21
rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32])
total number of confs: 55
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071865 none CC1(NC(=O)C2=CNN=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 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]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 5, 5, 5, 1, 1, 15, 1, 1] 21
rigid atoms, others: [0, 1, 2, 32, 10, 11, 12, 20, 28, 29, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071865 none CC1(NC(=O)C2=CNN=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 11, 1, 1, 8, 8, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 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]
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: [15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 21, 21, 21, 21, 15, 15, 1, 15, 15] 21
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: 51
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071865 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071865
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071865/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071865
Building REAL250005071866
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071866'
/scratch/stefan/7916153/working/building/REAL250005071866 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071866

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071866/0 /scratch/stefan/7916153/working/building/REAL250005071866 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1003)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1003
`/scratch/stefan/7916153/working/3D/1003' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071866.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071866.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071866/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071866 none COCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens need rotated
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [129, 129, 80, 66, 17, 17, 17, 14, 14, 14, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 129, 129, 129, 122, 120, 94, 94, 66, 66, 17, 14, 14, 14, 14, 13, 1, 14, 14] 129
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: 592
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071866 none COCCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens need rotated
129  conformations in input
total number of sets (complete confs): 129
using faster count positions algorithm for large data
unique positions, atoms: [89, 71, 30, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 89, 89, 89, 63, 66, 39, 39, 19, 19, 3, 2, 2, 2, 1, 1, 14, 1, 1] 129
rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 402
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071866 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071866
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071866/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071866
Building REAL250005071867
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071867'
/scratch/stefan/7916153/working/building/REAL250005071867 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071867

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071867/0 /scratch/stefan/7916153/working/building/REAL250005071867 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1004)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1004
`/scratch/stefan/7916153/working/3D/1004' -> `0.mol2'
Preparing input files

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

`REAL250005071867.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071867.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071867/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071867 none CC1(NC(=O)C2=NOC=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 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]
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, 8, 8, 1, 8, 1, 1, 1, 1, 1, 13, 13, 13, 26, 26, 31, 31, 31, 31, 31, 13, 13, 13, 13, 8, 1, 1, 13, 13, 31, 13, 13] 31
rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071867 none CC1(NC(=O)C2=NOC=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 2, 2, 2, 3, 13, 13, 1, 1, 14, 1, 1] 31
rigid atoms, others: [0, 1, 2, 10, 11, 12, 20, 27, 28, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071867 none CC1(NC(=O)C2=NOC=C2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 22, 22, 22, 31, 31, 31, 31, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 31, 31, 14, 14, 1, 14, 14] 31
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 73
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071867 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071867
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071867/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071867
Building REAL250005071868
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071868'
/scratch/stefan/7916153/working/building/REAL250005071868 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071868

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071868/0 /scratch/stefan/7916153/working/building/REAL250005071868 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1005)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1005
`/scratch/stefan/7916153/working/3D/1005' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=C(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071868.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071868.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071868/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071868 none CCC=C(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
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, 90, 90, 18, 90, 18, 18, 12, 12, 12, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 93, 93, 93, 93, 93, 90, 90, 90, 90, 18, 12, 12, 12, 12, 12, 1, 12, 12] 93
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: 237
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071868 none CCC=C(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
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: [30, 18, 18, 3, 18, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 1, 30, 30, 30, 30, 30, 18, 18, 18, 18, 3, 2, 2, 2, 1, 1, 12, 1, 1] 93
rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 136
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071868 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071868
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071868/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071868
Building REAL250005071869
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071869'
/scratch/stefan/7916153/working/building/REAL250005071869 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071869

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071869/0 /scratch/stefan/7916153/working/building/REAL250005071869 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1006)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1006
`/scratch/stefan/7916153/working/3D/1006' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071869.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071869.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071869/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071869 none COC(C)C(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 3, 7, 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]
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, 22, 39, 22, 22, 19, 19, 19, 19, 10, 1, 10, 1, 1, 1, 1, 1, 1, 19, 40, 40, 40, 39, 39, 39, 39, 22, 19, 19, 19, 19, 19, 1, 19, 19] 40
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: 127
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071869 none COC(C)C(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 3, 7, 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]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [21, 17, 3, 17, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 21, 21, 21, 17, 17, 17, 17, 3, 2, 2, 2, 1, 1, 19, 1, 1] 40
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 95
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071869 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071869
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071869/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071869
Building REAL250005071870
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071870'
/scratch/stefan/7916153/working/building/REAL250005071870 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071870

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071870/0 /scratch/stefan/7916153/working/building/REAL250005071870 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1007)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1007
`/scratch/stefan/7916153/working/3D/1007' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071870.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071870.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071870/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071870 none CC(C)OCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 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]
0  hydrogens need rotated
125  conformations in input
total number of sets (complete confs): 125
using faster count positions algorithm for large data
unique positions, atoms: [125, 121, 125, 100, 29, 29, 29, 24, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 125, 125, 125, 125, 125, 125, 125, 100, 100, 29, 24, 24, 24, 24, 24, 1, 24, 24] 125
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: 396
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071870 none CC(C)OCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 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]
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: [66, 52, 66, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 66, 66, 66, 66, 66, 66, 66, 20, 20, 3, 2, 2, 2, 1, 1, 24, 1, 1] 125
rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 232
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071870 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071870
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071870/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071870
Building REAL250005071871
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071871'
/scratch/stefan/7916153/working/building/REAL250005071871 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071871

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071871/0 /scratch/stefan/7916153/working/building/REAL250005071871 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1008)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1008
`/scratch/stefan/7916153/working/3D/1008' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCOCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071871.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071871.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071871/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071871 none CCCOCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 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]
0  hydrogens need 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, 134, 83, 22, 22, 22, 18, 18, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 201, 201, 201, 201, 201, 175, 175, 83, 83, 22, 18, 18, 18, 18, 18, 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: 732
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071871 none CCCOCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 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]
0  hydrogens 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, 113, 57, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 155, 155, 155, 155, 155, 113, 113, 20, 20, 3, 2, 2, 2, 1, 1, 18, 1, 1] 201
rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 649
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071871 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071871
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071871/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071871
Building REAL250005071872
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071872'
/scratch/stefan/7916153/working/building/REAL250005071872 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071872

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071872/0 /scratch/stefan/7916153/working/building/REAL250005071872 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1009)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1009
`/scratch/stefan/7916153/working/3D/1009' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(NC(=O)C2CCOC2)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071872.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071872.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071872/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071872 none CC1(NC(=O)C2CCOC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 12, 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, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 17, 17, 17, 52, 52, 62, 62, 62, 62, 62, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 17, 17, 62, 17, 17] 62
rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36])
total number of confs: 171
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071872 none CC1(NC(=O)C2CCOC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 12, 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, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 17, 17, 17, 17, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 17, 17, 17, 17, 17, 17, 17, 1, 1, 19, 1, 1] 62
rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34])
total number of confs: 77
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071872 none CC1(NC(=O)C2CCOC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 12, 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, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 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
62  conformations in input
total number of sets (complete confs): 62
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 19, 29, 29, 29, 62, 62, 62, 62, 18, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 29, 62, 62, 62, 62, 62, 62, 62, 19, 18, 1, 19, 19] 62
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: 177
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071872 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071872
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071872/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071872
Building REAL250005071873
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071873'
/scratch/stefan/7916153/working/building/REAL250005071873 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071873

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071873/0 /scratch/stefan/7916153/working/building/REAL250005071873 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1010)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1010
`/scratch/stefan/7916153/working/3D/1010' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(OC)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071873.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071873.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071873/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071873 none CCC(OC)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 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]
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: [64, 60, 24, 60, 64, 24, 24, 22, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 69, 69, 69, 69, 69, 60, 64, 64, 64, 24, 22, 22, 22, 22, 22, 1, 22, 22] 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: 293
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071873 none CCC(OC)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 3, 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]
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: [20, 16, 3, 16, 23, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 25, 25, 25, 25, 25, 16, 23, 23, 23, 3, 2, 2, 2, 1, 1, 22, 1, 1] 69
rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 180
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071873 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071873
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071873/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071873
Building REAL250005071874
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071874'
/scratch/stefan/7916153/working/building/REAL250005071874 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071874

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071874/0 /scratch/stefan/7916153/working/building/REAL250005071874 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1011)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1011
`/scratch/stefan/7916153/working/3D/1011' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071874.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071874.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071874/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071874 none COC(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
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, 105, 124, 34, 34, 34, 26, 26, 26, 26, 12, 1, 12, 1, 1, 1, 1, 1, 1, 26, 126, 126, 126, 126, 126, 126, 126, 105, 105, 34, 26, 26, 26, 26, 26, 1, 26, 26] 126
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: 478
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071874 none COC(C)CC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
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: [55, 47, 22, 45, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 1, 55, 55, 55, 47, 47, 47, 47, 22, 22, 3, 2, 2, 2, 1, 1, 26, 1, 1] 126
rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 262
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071874 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071874
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071874/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071874
Building REAL250005071875
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071875'
/scratch/stefan/7916153/working/building/REAL250005071875 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071875

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071875/0 /scratch/stefan/7916153/working/building/REAL250005071875 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1012)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1012
`/scratch/stefan/7916153/working/3D/1012' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071875.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071875.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071875/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071875 none C=CCCC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 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]
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, 133, 104, 31, 31, 31, 25, 25, 25, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 133, 133, 133, 133, 133, 104, 104, 31, 25, 25, 25, 25, 24, 1, 25, 25] 133
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: 505
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071875 none C=CCCC(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 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]
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: [70, 36, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 70, 70, 70, 36, 36, 18, 18, 3, 2, 2, 2, 1, 1, 25, 1, 1] 133
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 306
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071875 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071875
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071875/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071875
Building REAL250005071876
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071876'
/scratch/stefan/7916153/working/building/REAL250005071876 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071876

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071876/0 /scratch/stefan/7916153/working/building/REAL250005071876 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1013)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1013
`/scratch/stefan/7916153/working/3D/1013' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071876.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071876.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071876/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071876 none CCOCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 3, 7, 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]
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, 123, 115, 84, 25, 25, 25, 22, 22, 22, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 128, 128, 128, 128, 128, 115, 115, 84, 84, 25, 22, 22, 22, 22, 21, 1, 22, 22] 128
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: 500
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071876 none CCOCCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 3, 7, 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]
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: [83, 70, 38, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 83, 83, 83, 83, 83, 38, 38, 19, 19, 3, 2, 2, 2, 1, 1, 22, 1, 1] 128
rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 327
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071876 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071876
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071876/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071876
Building REAL250005071877
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071877'
/scratch/stefan/7916153/working/building/REAL250005071877 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071877

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071877/0 /scratch/stefan/7916153/working/building/REAL250005071877 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1014)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1014
`/scratch/stefan/7916153/working/3D/1014' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071877.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071877.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071877/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071877 none COCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [83, 83, 65, 26, 65, 26, 26, 22, 22, 22, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 83, 83, 83, 83, 83, 65, 65, 65, 65, 26, 22, 22, 22, 22, 21, 1, 22, 22] 83
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: 307
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071877 none COCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 3, 7, 7, 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]
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: [56, 46, 19, 3, 19, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 56, 56, 56, 46, 46, 19, 19, 19, 19, 3, 2, 2, 2, 1, 1, 22, 1, 1] 83
rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 238
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071877 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071877
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071877/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071877
Building REAL250005071878
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071878'
/scratch/stefan/7916153/working/building/REAL250005071878 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071878

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071878/0 /scratch/stefan/7916153/working/building/REAL250005071878 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1015)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1015
`/scratch/stefan/7916153/working/3D/1015' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCOCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071878.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071878.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071878/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071878 none C=CCOCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 3, 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]
0  hydrogens need rotated
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, 82, 21, 21, 21, 17, 17, 17, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 201, 201, 201, 201, 201, 82, 82, 21, 17, 17, 17, 17, 17, 1, 17, 17] 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: 680
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071878 none C=CCOCC(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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]
dock color type numbers: [7, 7, 7, 3, 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]
0  hydrogens 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, 112, 49, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 154, 154, 154, 112, 112, 17, 17, 3, 2, 2, 2, 1, 1, 17, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34])
total number of confs: 546
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071878 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071878
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071878/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071878
Building REAL250005071879
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071879'
/scratch/stefan/7916153/working/building/REAL250005071879 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071879

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071879/0 /scratch/stefan/7916153/working/building/REAL250005071879 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1016)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1016
`/scratch/stefan/7916153/working/3D/1016' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(NC(=O)C2=COC=N2)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071879.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071879.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071879/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071879 none CC1(NC(=O)C2=COC=N2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 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]
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: [11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 11, 11, 11, 23, 23, 27, 27, 27, 27, 27, 11, 11, 11, 11, 6, 1, 1, 11, 11, 27, 11, 11] 27
rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31])
total number of confs: 75
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071879 none CC1(NC(=O)C2=COC=N2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 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]
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, 3, 11, 11, 11, 11, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 11, 11, 1, 1, 16, 1, 1] 27
rigid atoms, others: [0, 1, 2, 10, 11, 12, 20, 27, 28, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29])
total number of confs: 50
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071879 none CC1(NC(=O)C2=COC=N2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 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]
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: [16, 16, 16, 21, 21, 21, 27, 27, 27, 27, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 21, 27, 27, 15, 16, 1, 16, 16] 27
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 62
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071879 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071879
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071879/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071879
Building REAL250005071880
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071880'
/scratch/stefan/7916153/working/building/REAL250005071880 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071880

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071880/0 /scratch/stefan/7916153/working/building/REAL250005071880 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1017)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1017
`/scratch/stefan/7916153/working/3D/1017' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071880.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071880.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071880/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071880 none CCCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
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, 103, 92, 28, 92, 28, 28, 22, 22, 22, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 105, 105, 105, 105, 105, 103, 103, 92, 92, 92, 92, 28, 22, 22, 22, 22, 21, 1, 22, 22] 105
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: 395
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071880 none CCCC(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
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, 37, 20, 3, 20, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 43, 43, 43, 42, 43, 38, 38, 20, 20, 20, 20, 3, 2, 2, 2, 1, 1, 22, 1, 1] 105
rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 40, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 227
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071880 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071880
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071880/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071880
Building REAL250005071881
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071881'
/scratch/stefan/7916153/working/building/REAL250005071881 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071881

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071881/0 /scratch/stefan/7916153/working/building/REAL250005071881 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1018)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1018
`/scratch/stefan/7916153/working/3D/1018' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(NC(=O)CCC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071881.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071881.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071881/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071881 none CC1(NC(=O)CCC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 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, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [75, 42, 42, 7, 42, 3, 1, 1, 1, 1, 75, 75, 75, 184, 184, 201, 201, 201, 201, 201, 75, 75, 75, 75, 42, 7, 7, 3, 3, 1, 1, 1, 1, 1, 75, 75, 201, 75, 75] 201
rigid atoms, others: [32, 33, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 10, 11, 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: 596
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071881 none CC1(NC(=O)CCC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 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, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 19, 31, 75, 75, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 2, 2, 2, 3, 19, 19, 40, 40, 75, 75, 75, 75, 75, 1, 1, 24, 1, 1] 201
rigid atoms, others: [0, 1, 2, 35, 37, 38, 10, 11, 12, 34, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 352
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071881 none CC1(NC(=O)CCC2CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 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, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 36, 36, 36, 125, 155, 201, 201, 23, 7, 1, 7, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 36, 125, 125, 160, 160, 201, 201, 201, 201, 201, 24, 23, 1, 24, 24] 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: 818
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071881 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071881
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071881/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071881
Building REAL250005071882
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071882'
/scratch/stefan/7916153/working/building/REAL250005071882 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071882

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071882/0 /scratch/stefan/7916153/working/building/REAL250005071882 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1019)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1019
`/scratch/stefan/7916153/working/3D/1019' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(NC(=O)C2CC=CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071882.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071882.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071882/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071882 none CC1(NC(=O)C2CC=CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 1, 1, 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, 4, 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]
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: [22, 12, 12, 1, 12, 1, 1, 1, 1, 1, 22, 22, 22, 57, 57, 70, 70, 70, 70, 70, 22, 22, 22, 22, 12, 1, 1, 1, 1, 1, 1, 1, 22, 22, 70, 22, 22] 70
rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36])
total number of confs: 194
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071882 none CC1(NC(=O)C2CC=CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 1, 1, 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, 4, 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]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 22, 22, 22, 22, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 22, 22, 22, 22, 22, 22, 22, 1, 1, 22, 1, 1] 70
rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34])
total number of confs: 89
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071882 none CC1(NC(=O)C2CC=CC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 1, 1, 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, 4, 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]
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: [22, 22, 22, 31, 31, 31, 70, 70, 70, 70, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 31, 70, 70, 70, 70, 70, 70, 70, 22, 22, 1, 22, 22] 70
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: 181
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071882 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071882
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071882/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071882
Building REAL250005071883
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071883'
/scratch/stefan/7916153/working/building/REAL250005071883 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071883

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071883/0 /scratch/stefan/7916153/working/building/REAL250005071883 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1020)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1020
`/scratch/stefan/7916153/working/3D/1020' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(NC(=O)CC2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071883.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071883.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071883/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071883 none CC1(NC(=O)CC2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 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, 4, 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]
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: [53, 33, 33, 8, 33, 1, 1, 1, 1, 1, 53, 53, 53, 116, 116, 136, 136, 136, 136, 136, 53, 53, 53, 53, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 53, 53, 136, 53, 53] 136
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38])
total number of confs: 398
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071883 none CC1(NC(=O)CC2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 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, 4, 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]
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: [1, 1, 1, 3, 3, 3, 22, 53, 53, 53, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 22, 22, 53, 53, 53, 53, 53, 53, 53, 1, 1, 24, 1, 1] 136
rigid atoms, others: [0, 1, 2, 35, 37, 38, 10, 11, 12, 34, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 210
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071883 none CC1(NC(=O)CC2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 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, 4, 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]
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: [24, 24, 24, 39, 39, 39, 103, 136, 136, 136, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 39, 103, 103, 136, 136, 136, 136, 136, 136, 136, 24, 24, 1, 24, 24] 136
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: 507
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071883 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071883
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071883/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071883
Building REAL250005071884
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071884'
/scratch/stefan/7916153/working/building/REAL250005071884 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071884

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071884/0 /scratch/stefan/7916153/working/building/REAL250005071884 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1021)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1021
`/scratch/stefan/7916153/working/3D/1021' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)C1CC1)

`REAL250005071884.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071884.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071884/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071884 none CC(C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)C1CC1 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', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 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]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [59, 16, 16, 16, 14, 14, 14, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 59, 60, 60, 59, 59, 59, 59, 16, 14, 14, 14, 13, 14, 1, 14, 14, 60, 60, 60, 60, 60] 60
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, 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
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071884 none CC(C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)C1CC1 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', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 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]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 16, 17, 17, 16, 16, 16, 16, 3, 2, 2, 2, 1, 1, 14, 1, 1, 17, 17, 17, 17, 17] 60
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 17, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36, 37, 38])
total number of confs: 86
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071884 none CC(C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)C1CC1 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', 'C.3', 'C.3', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 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]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 12, 12, 12, 17, 17, 17, 17, 48, 48, 60, 60, 60, 60, 60, 17, 1, 1, 1, 3, 3, 3, 3, 12, 17, 17, 17, 17, 17, 60, 17, 17, 1, 1, 1, 1, 1] 60
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: 163
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071884 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071884
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071884/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071884
Building REAL250005071885
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071885'
/scratch/stefan/7916153/working/building/REAL250005071885 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071885

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071885/0 /scratch/stefan/7916153/working/building/REAL250005071885 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1022)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1022
`/scratch/stefan/7916153/working/3D/1022' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(C)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071885.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071885.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071885/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071885 none CC=C(C)C(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 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]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 24, 56, 24, 24, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 56, 56, 56, 56, 56, 56, 56, 24, 17, 17, 17, 17, 17, 1, 17, 17] 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: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071885 none CC=C(C)C(=O)NC1(C)CN(C(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 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]
dock color type numbers: [7, 7, 7, 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]
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: [18, 18, 3, 18, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 18, 18, 18, 18, 18, 18, 18, 3, 2, 2, 2, 1, 1, 17, 1, 1] 56
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 73
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071885 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071885
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071885/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071885
Building REAL250005071886
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071886'
/scratch/stefan/7916153/working/building/REAL250005071886 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071886

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071886/0 /scratch/stefan/7916153/working/building/REAL250005071886 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1023)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1023
`/scratch/stefan/7916153/working/3D/1023' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)NC2(C)CN(C(=O)C3=CC(=O)[N-]O3)C2)C1)

`REAL250005071886.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071886.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071886/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071886 none CC1CC(C(=O)NC2(C)CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 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, 7, 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]
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: [17, 17, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1, 17, 17, 17, 17, 17, 17, 17, 17, 3, 2, 2, 2, 1, 1, 16, 1, 1, 17, 17] 55
rigid atoms, others: [32, 33, 35, 36, 6, 7, 8, 9, 10, 11, 19] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 37, 38])
total number of confs: 72
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071886 none CC1CC(C(=O)NC2(C)CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 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, 7, 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]
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, 11, 11, 11, 17, 17, 17, 17, 49, 49, 55, 55, 55, 55, 55, 17, 1, 2, 2, 2, 1, 1, 1, 1, 11, 17, 17, 17, 17, 17, 55, 17, 17, 1, 1] 55
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: 156
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071886 none CC1CC(C(=O)NC2(C)CN(C(=O)C3=CC(=O)[N-]O3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', '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, 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, 7, 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]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 55, 23, 23, 23, 16, 16, 16, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 55, 55, 55, 55, 55, 55, 55, 55, 23, 16, 16, 16, 16, 16, 1, 16, 16, 55, 55] 55
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: 155
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071886 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071886
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071886/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071886
Building REAL250005071887
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071887'
/scratch/stefan/7916153/working/building/REAL250005071887 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071887

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071887/0 /scratch/stefan/7916153/working/building/REAL250005071887 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1024)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1024
`/scratch/stefan/7916153/working/3D/1024' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(NC(=O)C=C2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071887.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071887.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071887/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071887 none CC1(NC(=O)C=C2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 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, 4, 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]
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, 10, 10, 1, 10, 1, 1, 1, 1, 1, 21, 21, 21, 60, 60, 72, 72, 72, 72, 72, 21, 21, 21, 21, 10, 1, 1, 1, 1, 1, 1, 1, 21, 21, 72, 21, 21] 72
rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36])
total number of confs: 196
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071887 none CC1(NC(=O)C=C2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 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, 4, 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]
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, 3, 3, 3, 21, 21, 21, 21, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 1, 2, 2, 2, 3, 21, 21, 21, 21, 21, 21, 21, 1, 1, 18, 1, 1] 72
rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34])
total number of confs: 83
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071887 none CC1(NC(=O)C=C2CCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 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, 4, 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]
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: [18, 18, 18, 27, 27, 27, 72, 72, 72, 72, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 27, 72, 72, 72, 72, 72, 72, 72, 18, 18, 1, 18, 18] 72
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: 196
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071887 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071887
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071887/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071887
Building REAL250005071888
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071888'
/scratch/stefan/7916153/working/building/REAL250005071888 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071888

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071888/0 /scratch/stefan/7916153/working/building/REAL250005071888 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1025)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1025
`/scratch/stefan/7916153/working/3D/1025' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=C(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071888.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071888.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071888/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071888 none CC(C)=C(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 5, 1, 15, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [42, 42, 42, 22, 42, 22, 22, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 42, 42, 42, 42, 42, 42, 22, 15, 15, 15, 15, 15, 1, 15, 15] 42
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: 120
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071888 none CC(C)=C(F)C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 5, 1, 15, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 3, 13, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 13, 13, 13, 13, 13, 13, 3, 2, 2, 2, 1, 1, 15, 1, 1] 42
rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33])
total number of confs: 61
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071888 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071888
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071888/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071888
Building REAL250005071889
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071889'
/scratch/stefan/7916153/working/building/REAL250005071889 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071889

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071889/0 /scratch/stefan/7916153/working/building/REAL250005071889 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1026)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1026
`/scratch/stefan/7916153/working/3D/1026' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(NC(=O)C2=CCCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071889.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071889.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071889/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071889 none CC1(NC(=O)C2=CCCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 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, 4, 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]
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: [12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 12, 12, 30, 30, 37, 37, 37, 37, 37, 12, 12, 12, 12, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 37, 12, 12] 37
rigid atoms, others: [3, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36])
total number of confs: 104
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071889 none CC1(NC(=O)C2=CCCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 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, 4, 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]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 1, 1, 1, 6, 6, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 12, 12, 12, 12, 12, 12, 12, 1, 1, 15, 1, 1] 37
rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 10, 11, 12, 20] set([3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34])
total number of confs: 48
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071889 none CC1(NC(=O)C2=CCCC2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 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, 4, 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]
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: [15, 15, 15, 25, 25, 25, 37, 37, 37, 37, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 25, 37, 37, 37, 37, 37, 37, 37, 15, 15, 1, 15, 15] 37
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: 90
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071889 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071889
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071889/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071889
Building REAL250005071890
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071890'
/scratch/stefan/7916153/working/building/REAL250005071890 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071890

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071890/0 /scratch/stefan/7916153/working/building/REAL250005071890 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1027)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1027
`/scratch/stefan/7916153/working/3D/1027' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071890.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071890.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071890/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071890 none CC1(C)CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 1, 1, 17, 1, 1] 47
rigid atoms, others: [34, 35, 37, 38, 7, 8, 9, 10, 11, 12, 20] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 69
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071890 none CC1(C)CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 15, 39, 39, 47, 47, 47, 47, 47, 15, 1, 1, 1, 2, 2, 2, 1, 1, 1, 9, 15, 15, 15, 15, 15, 47, 15, 15] 47
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: 136
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071890 none CC1(C)CC1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 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]
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, 22, 22, 22, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 47, 47, 47, 47, 47, 47, 47, 47, 47, 22, 17, 17, 17, 17, 17, 1, 17, 17] 47
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: 129
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071890 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071890
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071890/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071890
Building REAL250005071891
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071891'
/scratch/stefan/7916153/working/building/REAL250005071891 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071891

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071891/0 /scratch/stefan/7916153/working/building/REAL250005071891 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1028)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1028
`/scratch/stefan/7916153/working/3D/1028' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C[C@@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071891.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071891.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071891/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071891 none CC1(C)C[C@@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 5, 7, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 3, 15, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 15, 15, 15, 15, 15, 15, 15, 15, 3, 2, 2, 2, 1, 1, 17, 1, 1] 47
rigid atoms, others: [34, 35, 37, 38, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 68
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071891 none CC1(C)C[C@@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 5, 7, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 15, 39, 39, 47, 47, 47, 47, 47, 15, 2, 2, 2, 2, 2, 2, 1, 1, 9, 15, 15, 15, 15, 15, 47, 15, 15] 47
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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071891 none CC1(C)C[C@@H]1C(=O)NC1(C)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 5, 7, 1, 11, 8, 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, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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]
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, 22, 47, 22, 22, 18, 18, 18, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 47, 47, 47, 47, 47, 47, 47, 47, 22, 18, 18, 18, 17, 17, 1, 18, 18] 47
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: 125
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071891 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071891
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071891/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071891
Building REAL250005071892
mkdir: created directory `/scratch/stefan/7916153/working/building/REAL250005071892'
/scratch/stefan/7916153/working/building/REAL250005071892 /scratch/stefan/7916153/working /scratch/stefan/7916153
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005071892

mkdir: created directory `0'
/scratch/stefan/7916153/working/building/REAL250005071892/0 /scratch/stefan/7916153/working/building/REAL250005071892 /scratch/stefan/7916153/working /scratch/stefan/7916153
Protomer 0 (index: 1029)
Found valid previously generated 3D confromation in /scratch/stefan/7916153/working/3D/1029
`/scratch/stefan/7916153/working/3D/1029' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(NC(=O)[C@@H]2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005071892.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005071892.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916153/working/building/REAL250005071892/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071892 none CC1(NC(=O)[C@@H]2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [21, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 21, 21, 21, 57, 57, 75, 75, 75, 75, 75, 21, 21, 21, 21, 12, 1, 1, 1, 1, 1, 1, 21, 21, 75, 21, 21] 75
rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36])
total number of confs: 194
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071892 none CC1(NC(=O)[C@@H]2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 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
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, 3, 3, 3, 21, 21, 21, 21, 21, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 2, 2, 2, 3, 21, 21, 21, 21, 21, 21, 1, 1, 25, 1, 1] 75
rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 11, 12, 13, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34])
total number of confs: 91
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005071892 none CC1(NC(=O)[C@@H]2CCCO2)CN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 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
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 36, 36, 36, 75, 75, 75, 75, 75, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 36, 75, 75, 75, 75, 75, 75, 24, 25, 1, 25, 25] 75
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: 203
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916153/working/building/REAL250005071892 /scratch/stefan/7916153/working /scratch/stefan/7916153

Finished preparing REAL250005071892
Recording results
/scratch/stefan/7916153/working /scratch/stefan/7916153
Appending to /scratch/stefan/7916153/finished/xaaaabh.*
0: /scratch/stefan/7916153/working/building/REAL250005071892/0.*
Removing working files in /scratch/stefan/7916153/working/building/REAL250005071892
/scratch/stefan/7916153
Compressing combined databse files
/scratch/stefan/7916153/finished/xaaaabh.db2.gz
/scratch/stefan/7916153/finished/xaaaabh.solv.gz


=======================================================
WARNING: STORE_PROTOMERS not executable or a directory!
All results left in place (/scratch/stefan/7916153/finished)
=======================================================

Finalizing...
removed `/scratch/stefan/7916153/working/3D/1030'
removed directory: `/scratch/stefan/7916153/working/3D'
`/scratch/stefan/7916153/working/protonate' -> `/scratch/stefan/7916153/archive'
`/scratch/stefan/7916153/working/input-smiles.ism' -> `/scratch/stefan/7916153/archive/input-smiles.ism'
rmdir: removing directory, `/scratch/stefan/7916153/working/building'
rmdir: removing directory, `/scratch/stefan/7916153/working'
ls: No match.
ls: No match.